Methods of evaluating response to cancer therapy

ABSTRACT

A method of evaluating a cancer patient comprising evaluating gene expression levels in a patient sample, calculating a predictor score using the gene expression levels, and assessing the likelihood of a therapeutic outcome using the predictor score is disclosed.

This application claims priority to U.S. Provisional application Ser. No. 61/324,166 filed Apr. 14, 2010, which is incorporated herein by reference in its entirety.

BACKGROUND OF THE INVENTION

I. Field of the Invention

Embodiments of this invention are directed generally to biology and medicine. In certain aspects the invention relates to a gene set whose levels of expression are evaluated and used to prognose and/or derive a survival indicator for a patient who has undergone therapy, who is undergoing therapy, or who is a candidate for therapy.

II. Background

There are four main approaches to improving the ability to predict responsiveness to therapies. One approach is a standard predictive or chemopredictive study focused on treatment, in which a sufficiently powered discovery population of subjects is used to define a predictive test that must then be proven to be accurate in a similarly sized validation population (Ransohoff, 2005; Ransohoff 2004). Several studies have used this approach to define predictive genes for adjuvant tamoxifen therapy (Ma et al., 2004; Jansen et al., 2005; Loi et al., 2005). There are advantages to this approach, particularly when samples are available from mature studies for retrospective analysis. But two disadvantages are that the study design is empirical and that adjuvant (post surgery) treatment introduces surgery as a confounding variable, because it is impossible to ever know which patients were cured by their surgery and would never relapse, irrespective of their sensitivity to systemic therapy. Neoadjuvant chemotherapy trials enable a direct comparison of tumor characteristics with pathologic response to the specific therapy (Ayers et al., 2004).

SUMMARY OF THE INVENTION

In medicine today, doctors search for methods of predicting how a patient (given their condition) may respond to treatment. Symptoms and tests may indicate favorable treatment with standard therapies. Likewise, a number of symptoms, health factors, and tests may indicate a less favorable treatment result with standard treatment—this may indicate that a more aggressive treatment plan may be desired. Prognostic scoring is also used for cancer outcome predictions.

Although pathologic complete response (pCR) has been adopted as the primary endpoint for neoadjuvant trials because it is associated with long-term survival, it has not been uniformly or consistently defined (Bear, 2006; Carey, 2005; Hennessy, 2005;

Kaufmann, 2006; Kuroi, 2005; Kurosumi, 2004; Rajan, 2004; von Minckwitz, 2005). While it is generally agreed that a definition of pCR should include patients without residual invasive carcinoma in the breast (pT0), the presence of nodal metastasis, minimal residual cellularity, and residual in situ carcinoma are not consistently stated as either pCR or residual disease (RD) (Bear, 2006; Kaufmann, 2006; Hennessy, 2005; Rajan, 2004). Therefore, dichotomization of response as pCR or residual disease (RD) may be simplistic for the objective of assay discovery and validation, particularly because residual disease (RD) after neoadjuvant treatment includes a broad range of actual tumor shrinkage. In some patients who are categorized as RD but actually show minimal residual disease, the response outcome blurs the prognostic distinction between pCR and RD. On the other hand, it should be possible to clearly identify patients within RD who are resistant to treatment in order to develop management strategies for this adverse outcome.

Expression markers are chosen for the ability to classify and/or identify patients as to probability for response (or non response) to therapy. Response to therapy is commonly classified by the RECIST criteria established by the World Health Organization, the National Cancer Institute and the European Organization for Research and Treatment of Cancer. The RECIST criteria classify response as progressive disease (PD), stable disease (SD), partial response (PR), and complete response (CR). A good response is typically considered to include PR+CR (collectively referred to herein as Objective Response).

Certain aspects of the invention include methods of evaluating a cancer patient comprising one or more of the steps of (a) evaluating gene expression levels in a patient sample comprising cancer cells or an RNA sample isolated from one or more a patient samples, wherein a plurality of genes to be evaluated are selected from 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90, 100, 150, or all of the genes identified in Table 2, Table 3, and Table 4, including all ranges and values there between and all subsets and combinations thereof (5, 10, 15, 20, 25, 100 or more such genes can be specifically excluded, including all values and ranges there between); (b) calculating a predictor score using a gene expression profile index; and (c) assessing the likelihood of a therapeutic outcome using the predictor score. The method may further comprise classifying a patient prior to evaluation. In certain aspects classification can include identifying a cancer patient with a disease state classified as a residual disease state or other clinically defined state prior to evaluation. In certain aspects, a predictor includes but is not limited to a measure for distant relapse-free survival (DRFS).

In still a further aspect, a gene expression index comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90, 100, 150 or all of the genes identified in Table 2, Table 3, and Table 4 including all values and ranges there between as well as a number of subsets of these genes which may include some genes from one or more tables and exclude others from the same table or other tables.

In other aspects, a patient may be stratified or analyzed by using other factors such as protein expression, demographic information, family history, and other biological or medical states. The method may include determining Her2-neu and/or estrogen receptor status of the patient sample and/or evaluation of tumor size, cellularity of tumor bed, and/or nodal burden to name a few.

The methods may also provide a treatment recommendation depending on the assessment derived from analysis of the gene expression profile as well as other factors. In certain aspects the recommendation may be based on residual cancer burden (RCB) classification or the like. A treatment is typically a standard treatment or a more aggressive non-standard treatment depending on the analysis. For example a treatment may be combination of one or more cancer therapies, such as hormonal therapy and/or chemotherapy. Hormonal therapy includes, but is not limited to tamoxifen therapy, aromatase inhibitor therapy, or SERM therapy.

In other aspects, preparing a gene expression index can include one or more of the following steps: (a) obtaining data associated with a plurality of cancer patients, such as breast cancer, melanoma, ovarian cancer, testicular cancer or the like comprising measuring expression levels of a plurality of genes in samples from a plurality of patients; (b) partitioning the data into a first and second dataset; (c) evaluating the data and identifying data associated with a particular treatment outcome; (d) selecting a set of genes whose expression levels are indicative of therapeutic outcome. In one aspect, the index includes evaluation of survival of the patient population sampled for all or part of the reference population of tumor samples such as the distant relapse-free survival (DRFS) of the patient population.

Other aspects of the invention include kits to determine responsiveness of a cancer or cancer patient to a treatment or therapy comprising one or more of (a) reagents for determining expression levels of a plurality of genes selected from Table 2, Table 3, and Table 4 or combinations thereof, such as probe sets that identify and measure the levels of gene transcripts, transcription, or protein levels; and software encoding methods for designing, gathering, inputting, analyzing and/or assessing various data, which includes an algorithm for calculating a predictor score based on the analysis of the gene expression levels.

In still other aspects the invention includes an apparatus, or system for providing assessment of a sample relative to a gene expression index, the system comprising (a) an application server comprising an input manager to receive expression data from a user for a plurality of genes selected from Table 2, Table 3, and Table 4 or combinations thereof obtained from a patient sample or an RNA sample from such patient sample; and (b) a network server comprising an output manager constructed and arranged to provide an assessment to the user.

In yet another aspect the invention includes a computer readable medium having software modules for performing the one or more of the methods described herein comprising the acts of: (a) comparing gene expression data obtained from a patient sample for a plurality of genes selected from Table 2, Table 3, and Table 4 or combinations thereof with a reference; and (b) providing a predictor score to a physician for use in determining an appropriate therapeutic regimen for a patient.

In still yet another aspect the invention includes a computer system, having a processor, memory, external data storage, input/output mechanisms, a display, for performing the method of the invention, comprising (a) a database; (b) logic mechanisms in the computer for generating the transcriptional profile index; and (c) a comparing mechanism in the computer for comparing the gene expression reference to expression data from a patient sample or an RNA sample from such a patient sample to calculate a predictor score.

An internet accessible portal may be use to provide biological information constructed and arranged to execute a computer-implemented methods for providing: (a) a comparison of gene expression data of a plurality of genes of claim 1 in a patient sample with a transcriptional profile index; and (b) providing a predictor score to a physician for use in determining an appropriate therapeutic regime for a patient.

Other embodiments of the invention are discussed throughout this application. Any embodiment discussed with respect to one aspect of the invention applies to other aspects of the invention as well and vice versa. The embodiments in the Example section are understood to be embodiments of the invention that are applicable to all aspects of the invention.

The terms “inhibiting,” “reducing,” or “prevention,” or any variation of these terms, when used in the claims and/or the specification includes any measurable decrease or complete inhibition to achieve a desired result.

The use of the word “a” or “an” when used in conjunction with the term “comprising” in the claims and/or the specification may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one,” and “one or more than one.”

Throughout this application, the term “about” is used to indicate that a value includes the standard deviation of error for the device or method being employed to determine the value.

The use of the term “or” in the claims is used to mean “and/or” unless explicitly indicated to refer to alternatives only or the alternatives are mutually exclusive, although the disclosure supports a definition that refers to only alternatives and “and/or.”

As used in this specification and claim(s), the words “comprising” (and any form of comprising, such as “comprise” and “comprises”), “having” (and any form of having, such as “have” and “has”), “including” (and any form of including, such as “includes” and “include”) or “containing” (and any form of containing, such as “contains” and “contain”) are inclusive or open-ended and do not exclude additional, unrecited elements or method steps.

Other objects, features and advantages of the present invention will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples, while indicating specific embodiments of the invention, are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from this detailed description.

DESCRIPTION OF THE DRAWINGS

The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present invention. The invention may be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein.

FIG. 1 Plot of relapse-free survival in predicted responders and non-responders using the relapse-based predictor of Example 2 in the validation cohort of patients.

FIG. 2 Plot of distant relapse-free survival outcomes in predicted responders and non-responders using response-based endpoint of RCB0/I of Example 4 in the validation cohort of patients.

FIG. 3 Prediction of responders to chemotherapy in ER-positive tumors (A) and ER-negative tumors (B) using the response-based predictor in the validation cohort of patients.

FIG. 4 Prediction of responders to chemotherapy using a combination of relapse- and response-based predictors in the validation cohort of patients.

FIG. 5 Prediction of responders to chemotherapy in ER-positive tumors (A) and ER-negative tumors (B) using the combination of relapse- and response-based predictors in the validation cohort of patients.

FIG. 6 Endocrine sensitivity index in the validation cohort of patients.

FIG. 7 Plot of combined predictions in the validation cohort to identify responders and non-responders to chemotherapy.

FIG. 8 Plot of distant relapse-free survival within ER-specific subsets of the validation cohort, (A) ER-positive patients stratified by predicted responders and non-responders, (B) ER-negative patients stratified by predicted responders and non-responders.

FIG. 9 The decision algorithm that was used in the genomic test to predict a patient's sensitivity to adjuvant chemotherapy or chemo-endocrine therapy from a biopsy of newly diagnosed invasive breast cancer. (*) predicted sensitivity to endocrine therapy was defined as high or intermediate genomic sensitivity to endocrine therapy (SET) index; (**) predicted resistance to chemotherapy was defined as predicted extensive residual cancer burden (RCB-III) or predicted distant relapse or death within 3 years of diagnosis; (***) predicted sensitivity to chemotherapy was defined as predicted pathologic complete response (pCR) or minimal residual cancer burden (RCB-I).

FIG. 10 Plot of responders and non-responders in the validation cohort of patients predicted by using a combination of predictors of relapse, response as RCB-0/I, resistance as RCB-III, and SET. Kaplan-Meier estimates of distant relapse-free survival according to genomic predictions (before treatment) as treatment-sensitive (Rx Sensitive) or treatment-insensitive (Rx Insensitive) in the discovery (A) and independent validation (B) cohorts. For comparison, the prognosis of the groups stratified by actual pathologic response (pathologic complete response vs. residual disease) after completion of all chemotherapy is shown for the validation cohort (C). P-values are from the log-rank test. Vertical ticks on the curves indicate censored observations.

FIG. 11 Subset analysis of genomic predictions in the validation cohort: ER+/HER2-(A), ER-/HER2-(B), taxane chemotherapy administered as 12 cycles of weekly paclitaxel (C) or 4 cycles of 3-weekly docetaxel (D). P-values are from the log-rank test. Vertical ticks on the curves indicate censored observations.

FIG. 12 Kaplan-Meier estimates of distant relapse-free survival in the discovery cohort (A-D) and the independent validation cohort (E-H) of patients treated with sequential taxane-anthracycline chemotherapy, then endocrine therapy if hormone receptor-positive, stratified by other signatures reported to be predictive of response to neoadjuvant taxane-anthracycline chemotherapy. A prognostic signature for genomic grade index predicts pathologic response if high GGI versus low GGI (A, E); the intrinsic subtype classifier predicts pathologic response if basal-like or luminal B versus other subtypes (B, F); a genomic predictor of pathologic complete response (pCR) versus residual disease following taxane-anthracycline chemotherapy (C, G); and the genomic predictor of excellent pathologic response (pCR or RCB-I) versus other residual disease, according to ER status, that we incorporated in the last step of our prediction algorithm (D, H). P-values are from the log-rank test. Vertical ticks on the curves indicate censored observations.

FIG. 13 Schematic of use of the predictor assay to guide decisions in therapy outcome.

DETAILED DESCRIPTION OF THE INVENTION

Despite the critical importance of selecting the most effective adjuvant/neoadjuvant chemotherapy for an individual, diagnostic tests to guide selection of the optimal regimen for a particular patient continue to be inadequate (Carlson, 2000; Goldhirsch, 2003). Estrogen receptor (ER) negative status, high grade and high proliferative activity are histological characteristics that tend to indicate more chemotherapy sensitive cancer (Bast, 2001; Ross, 2003; Rouzier, 2005). However, although these clinicopathologic variables may identify eligibility or predict general chemotherapy sensitivity, they have little potential to guide selection of a specific treatment regimen in standard-of-care practice.

The limited utility of individual markers to predict clinical outcome of cancer may be due to the incomplete understanding of the function of these markers. In addition, biologically important molecules act in concert and form complex, interactive pathways where an individual molecule may only contribute limited information on the functional activity of a whole pathway. The promise of microarray technology is that, by assessing the transcriptional activity of a large number of genes, the complex gene-expression profile may contain more information than any individual marker that contributes to it.

There are examples indicating that the molecular classification of cancer based on gene-expression profiles could be important in framing patient management strategies. Unsupervised clustering of breast cancer specimens consistently separated tumors into ER⁺ and ER⁻ clusters (Gruvberger, 2001; Perou, 2000; Pusztai, 2003). Analysis of gene-expression profiles also distinguished sporadic breast cancers from breast cancer gene, BRCA, mutant cases (Hedenfalk, 2001). Transcriptional profiles have also revealed previously unrecognized molecular subgroups within existing histological categories in breast cancer (Perou, 2000), diffuse large-B-cell lymphoma, and soft tissue and central nervous system embryonal tumors (Nielsen, 2002; Pomeroy, 2002). In addition, gene-expression profiles have been shown to predict survival of patients with node-negative breast cancer (van de Vijver, 2002; van't Veer, 2002), lymphoma (Alizadeh, 2000; Rosenwald, 2002), renal cancer (Takahashi, 2001), and lung cancer (Beer, 2002).

Previous efforts into applying gene expression-based predictors in breast cancer have focused largely on predicting a patient's risk of cancer recurrence in the event of either receiving no systemic treatment after surgery (van de Vijver, 2002; van't Veer, 2002; Wang, 2005) or receiving tamoxifen, a hormonal therapy agent, for 5 years after surgery (Paik, 2006; Paik, 2004; Ma, 2006; Davis, 2007). These gene-based predictors do not directly address the need or the responsiveness to chemotherapy although a high risk of recurrence may indirectly suggest the general consideration of chemotherapy among the available options for patient management.

Other research efforts have also reported gene-based predictors of response to standard breast cancer treatments (Ayers, 2004; Bild, 2006; Chang, 2003; Hess, 2006; Modlich, 2006) although these are not commercially marketed yet as assays. Some of these predictors are developed using patient tissue samples treated clinically with a specific chemotherapy regimen and subsequently comparing genomic profiles of responders versus non-responders using survival-driven endpoints (Ayers, 2004; Chang, 2003; Hess, 2006; Modlich, 2006) whereas others are focused on analyses of changes in genes within breast cancer cell lines that are treated in vitro with single standard therapeutic agents (Bild, 2006).

As an in vivo model for marker development and validation, neoadjuvant (preoperative) chemotherapy provides an opportunity to gain access to samples that directly describe tumor response to therapy. Furthermore, complete eradication of all invasive cancer from the breast and regional lymph nodes, called pathologic complete response (pCR), is associated with excellent long-term cancer-free survival (Fisher, 1998; Kuerer, 1999). Therefore, the goal in developing treatment-directed response markers is to evaluate gene expression profiles in order to predict who may achieve pCR versus residual disease (RD). Pathologic CR is a meaningful clinical end-point to predict because these patients experience prolonged disease-free and overall survival compared to patients with lesser response (Cleator, 2005; Fisher, 1998; Kaufmann, 2006; Wolmark, 2001). Good survival in these patients reflects benefit from chemotherapy since most clinical and gene expression variables that are associated with pCR high grade, ER-negative status, high OncotypeDX recurrence score) tend to predict worse prognosis in the absence of chemotherapy (Paik, 2006; Paik, 2004).

Previous work has demonstrated the development and validation of a 30-probe genomic predictor for response to a taxane-containing chemotherapy (Ayers, 2004; Hess, 2006). The treatment administered in the neoadjuvant setting was sequential paclitaxel anthracycline preoperative chemotherapy (T/FAC). A complex multidrug regimen was selected for study because combination chemotherapy represents the current clinical standard for patients who require systemic cytotoxic treatment. Also, studies that explore gene signatures for response to individual drugs may not fully capture sensitivity to combination chemotherapy as practiced in standard-of-care.

A cohort of 82 patients was used for predictor discovery of pCR to preoperative T/FAC chemotherapy using fine needle biopsies taken before treatment and by analyzing gene profiles generated from a commercially available standard gene expression profiling technology (Affymetrix, Santa Clara, Calif.). Although several analytic techniques and resulting gene sets for response prediction were studied, the nominally best predictor for pCR with the least number of genes, called DLDA-30, was selected for independent validation in 51 additional patients. The predictor showed substantially higher sensitivity (a measure of how well a predictor identifies responsiveness or non-responsiveness to a therapy, e.g., true positives/(true positives+false negatives)) (92% vs. 61%) and slightly better negative predictive value (NPV, the proportion of patients with negative test results who are correctly diagnosed.) (96% vs. 86%) than a clinical predictor based on ER, grade and age (Hess, 2006). The positive predictive value (PPV, is the proportion of patients with positive test results who are correctly diagnosed.) of the genomic predictor at 52% (95 CI: 30%-73%), was significantly higher than the baseline 26% pCR rate in unselected patients. A sensitivity of 100% means that the test recognizes all patient as either responsive to therapy or non-responsive to therapy. Typically, sensitivity alone does not tell us how well the test predicts other classes (that is, about the negative cases). Sensitivity is not the same as the positive predictive value (ratio of true positives to combined true and false positives), which is as much a statement about the proportion of actual positives in the population being tested as it is about the test. The calculation of sensitivity typically does not take into account indeterminate test results. If a test cannot be repeated, the options are to exclude indeterminate samples from analyses (but the number of exclusions should be stated when quoting sensitivity), or, alternatively, indeterminate samples can be treated as false negatives (which gives the worst-case value for sensitivity and may therefore underestimate it).

Although this predictor and others described in literature (Chang, 2003; Modlich, 2006) may help define a patient population that is more likely to achieve pCR than the general patient population, further developments can help refine prediction of treatment response considerably. Although pCR as a response endpoint is strongly correlated with high treatment-related survival, patients with residual disease (RD) after treatment encompass a wide range of outcomes ranging from very good prognosis (“near-pCR”) to drug resistance. Predictors that can better classify response outcomes to capture and differentiate the high responders and non-responders within the spectrum of residual disease could significantly benefit patient management.

Although pathologic complete response (pCR) has been adopted as the primary endpoint for neoadjuvant trials because it is associated with long-term survival, it has not been uniformly or consistently defined (Bear, 2006; Carey, 2005; Hennessy, 2005; Kaufmann, 2006; Kuroi, 2005; Kurosumi, 2004; Rajan, 2004; von Minckwitz, 2005). While it is generally agreed that a definition of pCR should include patients without residual invasive carcinoma in the breast (pT0), the presence of nodal metastasis, minimal residual cellularity, and residual in situ carcinoma are not consistently stated as either pCR or residual disease (RD) (Bear, 2006; Kaufmann, 2006; Hennessy, 2005; Rajan, 2004). Therefore, dichotomization of response as pCR or residual disease (RD) may be simplistic for the objective of assay discovery and validation, particularly because residual disease (RD) after neoadjuvant treatment includes a broad range of actual tumor shrinkage. In some patients who are categorized as RD but actually show minimal residual disease, the response outcome blurs the prognostic distinction between pCR and RD. On the other hand, it should be possible to clearly identify patients within RD who are resistant to treatment in order to develop management strategies for this adverse outcome.

A measure of residual disease or residual cancer burden (RCB), previously developed and reported, may be useful as a variable to characterize response to treatment (Symmans et al., 2007). This measure is derived from the primary tumor dimensions, cellularity of the tumor bed, and axillary nodal burden. Each component contributes meaningful pathologic information and can be obtained using routine pathologic materials and methods of interpretation that could easily be implemented in routine diagnostic practice. RCB measurements can provide a continuous parameter of residual disease and thus of response or resistance, so that all subject responses contribute to the analysis.

RCB is divided into four survival-related classes (RCB-0 to RCB-III) where patients with minimal residual disease (RCB-I) have the same 5-year relapse-free survival as those with pCR (RCB-0), irrespective of the type of neoadjuvant chemotherapy administered, adjuvant hormonal therapy or the pathologic stage of RD. Therefore, the combination of RCB-0 (pCR) and RCB-I expands the subset of patients who can be identified as having “good response” and to have benefited from the chemotherapy. Extensive residual disease (RCB-III), on the other hand, is associated with poor prognosis, irrespective of the type of neoadjuvant chemotherapy administered, adjuvant hormonal therapy, or the pathologic stage of RD. In particular, all patients with RCB-III after T/FAC chemotherapy, who did not receive adjuvant hormonal therapy, suffered distant relapse within 3 years (Symmans et al., 2007). This identifies an important subset of patients who are not responsive to chemotherapy, or with residual disease (after surgery) that is too extensive to be controlled by hormonal therapy alone.

Therefore, residual cancer burden (RCB) is an informative tool and a metric to help develop response predictors based on better characterization of likely treatment outcomes. RCB categories can be employed with existing methods to define surrogate endpoints from neoadjuvant trials. As a metric correlated with survival, RCB is strongly and independently prognostic and the classes of RCB capture distinct sets of survival-based outcomes. Development of a predictor that reports likelihood of a patient's tumor post-treatment to belong to one of the RCB classes, rather than simply pCR as an endpoint, can yield valuable diagnostic information for efficient treatment management. In certain aspects, predictors specific to RCB-0 (pCR or complete response), RCB-0/I (pCR+near-pCR called good response) and RCB-III (resistance) are developed. In certain aspects of the methods described, the inventors have also accounted for tumor sub-types based on the status of two receptors, Her2-neu and ER, allowing for the predictors to capture heterogeneity within breast cancers and achieve acceptable diagnostic performance.

III. Predictors of Response or Resistance to Therapy

Sets of genes are defined that are prognostic, diagnostic, or predictive or indicative of the outcome for a cancer patient. These genes can be incorporated into an index or predictor of such an outcome and used in the management of the treatment for a given patient. Prognosis is a medical term denoting the doctor's prediction of how a patient's disease will progress, and whether there is chance of recovery.

Outcome can be represented in various forms to indicate probability of survival or likely survival outcome. In biostatistics, survival rate is a part of survival analysis, indicating the percentage of people in a study or treatment group who are alive for a given period of time after diagnosis. Survival rates are important for prognosis; for example, whether a type of cancer has a good or bad prognosis can be determined from its survival rate or survival outcome.

Patients with a certain disease can die directly from that disease or from an unrelated cause such as a car accident. When the precise cause of death is not specified, this is called the overall survival rate or observed survival rate. Doctors often use mean overall survival rates to estimate the patient's prognosis. This is often expressed over standard time periods, like one, five, and ten years. For example, prostate cancer has a much higher one year overall survival rate than pancreatic cancer, and thus has a better prognosis.

When someone is more interested in how survival is affected by the disease, there is also the net survival rate, which filters out the effect of mortality from other causes than the disease. Typically, the two main ways to calculate net survival arc relative survival and cause specific survival or disease specific survival.

Relative survival is calculated by dividing the overall survival after diagnosis of a disease by the survival as observed in a similar population that was not diagnosed with that disease. A similar population is composed of individuals with at least age and gender similar to those diagnosed with the disease. Cause-specific survival is calculated by treating deaths from other causes than the disease as withdrawals from the population that don't lower survival, comparable to patients who are not observed any longer, e.g. due to reaching the end of the study period. Relative survival has the advantage that it does not depend on accuracy of the reported cause of death; cause-specific survival has the advantage that it does not depend on the ability to find a similar population of people without the disease.

Survival is not the only endpoint that can be used as a metric in developing predictors such as those described herein. Endpoints or therapeutic outcomes can include survival or distant relapse-free survival (DRFS). Other endpoints are discussed in Cooper and Kaanders, Biological surrogate end-points in cancer trials: Potential uses, benefits and pitfalls, European Journal of Cancer, Volume 41, Issue 9, Pages 1261-1266, which is incorporated herein by reference. A “surrogate marker” or “surrogate endpoint” or “secondary endpoint” typically will refer to a biological or clinical parameter that is measured in place of the biologically definitive or clinically most meaningful parameter, i.e., survival. Primary endpoints may also include limitation of pharmacologic therapies, reduction of time to death, or reduction in the progression of the disease, disorder, or condition. Surrogate markers are pathophysiologic parameters determined by medical or clinical laboratory diagnosis that arc associated and have been correlated with the prognosis, progression, predisposition, or risk analysis with a disease, disorder, or condition that are not directly related to the primary diagnosed pathophysiologic condition. Secondary endpoints are those that supplement the primary endpoint. For example, secondary endpoints include reduction in pharmacologic therapy, reduction in requirement of a medical device, or alteration of the progression of the disease disorder, or condition. Typically, a clinical endpoint may refer to a disease, symptom, or sign that constitutes one of the target outcomes of the therapy or clinical trial. The results of a therapy or clinical trial generally indicate the number of people enrolled who reached the pre-determined clinical endpoint during the study interval, compared with the overall number of people who were enrolled. Once a patient reaches the endpoint, he or she is generally excluded from further experimental intervention (the origin of the term endpoint). For example, a clinical trial investigating the ability of a medication to prevent heart attack might use chest pain as a clinical endpoint. Any patient enrolled in the trial who develops chest pain over the course of the trial, then, would be counted as having reached that clinical endpoint. The results would ultimately reflect the fraction of patients who reached the endpoint of having developed chest pain, compared with the overall number of people enrolled. When an experiment involves a control group, the fraction of individuals who reach the clinical endpoint after an intervention is compared with the fraction of individuals in the control group who reached the same clinical endpoint, thus reflecting the ability of the intervention to prevent the endpoint in question. Some studies will examine the incidence of a combined endpoint, which can merge a variety of outcomes into one group.

When building prediction rules of treatment response or disease state in general from gene expression data can be selected from a small subset of informative genes that will be used as prognostic features in the predictor. Most predictors employ univariate filtering to rank the candidate genes according to the p-value of a two-sample unequal variance t-test comparing the mean expression values of each gene in the two response classes (e.g., pCR and RD). Univariate filtering methods have the disadvantage that they do not deal well with redundant features (genes that have similar expression profiles) and therefore the resulting predictors tend to be less robust (Lai, 2006).

The method used to identify predictive genes involved first, applying a filter to the gene expression data of all probes on an array to select the top probe sets to be used in signature development using the above described algorithm. Gene filtering can be based on the regularized t-test for the selected response endpoint such as pCR or RCB-0 (complete response), RCB-0/I (good response), or RCB-III (poor response). Other methods for gene filtering include methods that utilize non-specific global filtering criteria. These include, but are not limited to intensity-based filtering, which aims to remove genes that are not expressed at all in the samples studied or variability-based filtering, which aims to remove genes with low variability across samples.

A multivariate method was used to simultaneously select the signature genes and to calculate the classification score. The predictor is determined by level of penalization, which determines the number of genes included in the predictive signature, and the choice of a decision threshold to dichotomize the classification score. As one example, the inventors selected the maximum level of penalization resulting in the smallest signatures that yield significant cross-validated predictor or outcome predictor, each of these terms can be used interchangeably, performance—this step determines the signature probe sets and their weights. Then, a decision threshold is selected in order to optimize the predictive values of the predictor. Evaluation of the predictors was based on the joint confidence interval of the positive predictive value (PPV) and the negative predictive value (NPV) of the predictor at 5% significance level (low 95% confidence limit of PPV≧baseline response rate & low 95% confidence limit of NPV≧1—baseline response rate).

In developing the RCB-based predictor, the inventors used an approach that combines feature selection and model discovery using a multivariate penalized approach, an example of which is Gradient Directed Regularization developed by Prof. J. Friedman at Stanford University, a description of which can be found on the World Wide Web at stat.stanford.edu/˜jhf/ftp/pathlite.pdf. Typically, the informative genes are selected with penalization using the maximization of the area under the receiver operating characteristic (ROC) curve (AUC) as the optimization criterion. Ma and Huang have previously used a similar approach for disease classification (Ma, 2006). A receiver operating characteristic (ROC), or simply ROC curve, is a graphical plot of the sensitivity vs. (1—specificity) for a binary classifier system as its discrimination threshold is varied. The ROC can also be represented equivalently by plotting the fraction of true positives (TPR=true positive rate) vs. the fraction of false positives (FPR=false positive rate). The best possible prediction method would yield a point in the upper left corner or coordinate (0,1) of the ROC space, representing 100% sensitivity (all true positives are found) and 100% specificity (no false positives are found). The (0,1) point is also called a perfect classification. A completely random guess would give a point along a diagonal line (the so-called line of no-discrimination) from the left bottom to the top right corners. The diagonal line divides the ROC space in areas of good or bad classification/diagnostic. Points above the diagonal line indicate good classification results, while points below the line indicate wrong results.

As an example of predictor discovery and evaluation the protocol suggested by Wessels et al. was followed (Wessels, 2005). The methodology is briefly explained below. First, the input dataset is randomly partitioned into a training set and a test set. A 3-fold cross-validation based on Dudoit et al. recommendation of a 2:1 split between training and test sets was used (Dudoit, 2002). The training set consisting of ⅔ of the original data is used to develop a predictor. To account for bias in the several data-dependent decisions involved in building the predictor, a 5-fold internal cross-validation can be used to select the optimal set of genes for the predictor and to tune the parameters of the predictor, e.g., the degree of penalization. Since different optimal reporter gene sets might result from the different internal cross-validation folds, the number of times each gene is selected is tracked to provide a measure of its importance or its reliability. The trained predictor is then tested on the ⅕ hold-out part of the training dataset and its performance is evaluated based on the AUC.

To obtain a less biased estimate of classification performance, the trained predictor or outcome predictor can be evaluated on the test set (⅓ of the original data) that was not used in training the predictor. To assess the significance of the predictive performance of the trained predictor, the permutation predictive performance of the predictor was estimated by randomly scrambling the outcome labels in the test dataset. The entire process of randomly splitting the data to a training and a test set was repeated a number of times to obtain the distributions and summary statistics of the performance metrics.

Typically, under cross-validation the decision threshold is varied along all possible values and for each value predictor performance (accuracy, positive predictive value (PPV), negative predictive value (NPV)) is determined. The threshold is selected that yields the best compromise between PPV and NPV, as typically increasing PPV results in decreasing NPV. Typically, the objective is to maximize both.

In certain aspects, other measurements or determinations can be made in conjunction the nucleic acid analysis, for example determination of protein expression and/or histology of a sample. Protein expression can be detected in tumor tissue, cell material obtained by biopsy and the like. For example, a biopsy sample can be immobilized and contacted with an antibody, an antibody fragment or an aptamer that binds selectively to the protein to be detected. The sample can be assayed to determine whether the antibody, fragment or aptamer has bound to the protein by techniques well known in the art. Protein expression can be measured by a variety of methods including but not limited to Western blot, immunoblot, enzyme-linked immunosorbant assay (ELISA), radioimmunoassay (RIA), immunoprecipitation, surface plasmon resonance, immunohistochemical (IHC) analysis, mass spectrometry, fluorescence activated cell sorting (FACS) and flow cytometry.

In a further aspect, IHC analysis is used to measure protein expression. The level of expression for a sample is determined by IHC by staining the sample for a particular expression marker and developing a score for the staining. For example, monoclonal antibodies can be used to stain for the expression of a marker of interest. Mouse antibodies are known for use in the staining of the marker PTEN. Samples can be evaluated for the frequency of cells stained for each sample and the intensity of the stain. Typically, a score based on the frequency (rated from 0-4) and intensity (rated from 0-4) of the stained sample is developed as a measure of overall expression. Exemplary but non-limiting methods for IHC and criteria for scoring expression are described in detail in Handbook of Immunohistochemistry and In Situ Hybridization in Human Carcinomas, M. Hayat Ed., 2004, Academic Press.

IV. Use of Predictor for Patient Evaluation

In one aspect of the invention, a predictor or transcriptional profile index is used to measure the expression of many genes that provide predictive information about a likely outcome for a particular patient. The invention includes the methods for standardizing the expression values of future samples to a normalization standard that will allow direct comparison of the results to past samples, such as from a clinical trial. The invention also includes the biostatistical methods to calculate and report such results. A sample as used herein can comprise any number of cells that is sufficient for a clinical diagnosis or prognosis, and typically contain at least, at most or about 100 target cells.

The microarrays provide a suitable method to measure gene expression from clinical samples. mRNA levels measured by microarrays, such as Affymetrix U133A gene chips, in fine needle aspirates (FNA), core needle biopsy, and/or frozen tumor tissue samples of breast cancer correlated closely with protein expression by enzyme immunoassay and by routine immunohistochemistry.

Estrogen receptor and Her2-neu status. ER-positive breast cancer includes a continuum of ER expression that might reflect a continuum of biologic behavior and endocrine sensitivity. Others have reported that some breast cancers are difficult to predict as ER-positive based on transcriptional profile and described non-estrogenic growth effects, such as HER-2, more frequently in this small subset of tumors with aggressive natural history (Kun et al., 2003). Indeed, ER mRNA levels are lower in breast cancers that are positive for both ER and HER2 (Konecny et al., 2003).

V. Cancer Therapies

Diagnostic tools are needed not merely for prognosis, but, for providing a biological rationale and to demonstrate clinical benefit when they are used to guide the selection and duration of therapies, particularly in light of the cost, complexity, toxicity, benefits and other factors related to such therapies. An index or predictor can be used to predict the likelihood of response rather than intrinsic prognosis.

In addition to other know methods of cancer therapy, hormone therapies may be employed in the treatment of patients identified as having hormone sensitive cancers. Hormones, or other compounds that stimulate or inhibit these pathways, can bind to hormone receptors, blocking a cancer's ability to get the hormones it needs for growth. By altering the hormone supply, hormone therapy can inhibit growth of a tumor or shrink the tumor. Typically, these cancer treatments only work for hormone-sensitive cancers. If a cancer is hormone sensitive, a patient might benefit from hormone therapy as part of cancer treatment. Sensitive to hormones is usually determined by taking a sample of a tumor (biopsy) and conducting analysis in a laboratory.

A. Chemotherapy

Chemotherapy is the use of chemical substances to treat disease. In its modern-day use, it refers to cytotoxic drugs used to treat cancer or the combination of these drugs into a standardized treatment regimen. There are a number of strategies in the administration of chemotherapeutic drugs used today. Chemotherapy may be given with a curative intent or it may aim to prolong life or to palliate symptoms.

Combined modality chemotherapy is the use of drugs with other cancer treatments, such as radiation therapy or surgery. Combination chemotherapy is a similar practice which involves treating a patient with a number of different drugs simultaneously, e.g., T/FAC therapy. Typically, the drugs differ in their mechanism and side effects. The biggest advantage is minimizing the chances of resistance developing to any one agent.

In neoadjuvant chemotherapy (preoperative treatment) initial chemotherapy is aimed for shrinking the primary tumor, thereby rendering local therapy (surgery or radiotherapy) less destructive or more effective.

Adjuvant chemotherapy (postoperative treatment) can be used when there is little evidence of cancer present, but there is risk of recurrence. This can help reduce chances of resistance developing if the tumor does develop. It is also useful in killing any cancerous cells which have spread to other parts of the body. This is often effective as the newly growing tumors are fast-dividing, and therefore very susceptible.

Palliative chemotherapy is given without curative intent, but simply to decrease tumor load and increase life expectancy. For these regimens, a better toxicity profile is generally expected.

All chemotherapy regimens require that the patient be capable of undergoing the treatment. Performance status is often used as a measure to determine whether a patient can receive chemotherapy, or whether dose reduction is required.

B. Hormone Therapy

Several malignancies respond to hormonal therapy. Strictly speaking, this is not chemotherapy. Cancer arising from certain tissues, including the mammary and prostate glands, may be inhibited or stimulated by appropriate changes in hormone balance. Cancers that are most likely to be hormone-receptive include: Breast cancer, Prostate cancer, Ovarian cancer, and Endometrial cancer. Not every cancer of these types is hormone-sensitive, however. That is why the cancer must be analyzed to determine if hormone therapy is appropriate.

Breast cancer cells often highly express the estrogen and/or progesterone receptor. Inhibiting the production (with aromatase inhibitors) or action (with tamoxifen) of these hormones can often be used as an adjunct to therapy.

Hormone therapy may be used in combination with other types of cancer treatments, including surgery, radiation and chemotherapy. A hormone therapy can be used before a primary cancer treatment, such as before surgery to remove a tumor. This is called neoadjuvant therapy. Hormone therapy can sometimes shrink a tumor to a more manageable size so that it's easier to remove during surgery.

Hormone therapy is sometimes given in addition to the primary treatment—usually after—in an effort to prevent the cancer from recurring (adjuvant therapy). In some cases of advanced (metastatic) cancers, such as in advanced prostate cancer and advanced breast cancer, hormone therapy is sometimes used as a primary treatment.

The most common types of drugs for hormone-receptive cancers include: (1) Anti-hormones that block the cancer cell's ability to interact with the hormones that stimulate or support cancer growth. Though these drugs do not reduce the production of hormones, anti-hormones block the ability to use these hormones. Anti-hormones include the anti-estrogens tamoxifen (Nolvadex) and toremifene (Fareston) for breast cancer, and the anti-androgens flutamide (Eulexin) and bicalutamide (Casodex) for prostate cancer. (2) Aromatase inhibitors —Aromatase inhibitors (AIs) target enzymes that produce estrogen in postmenopausal women, thus reducing the amount of estrogen available to fuel tumors. AIs are only used in postmenopausal women because the drugs can't prevent the production of estrogen in women who haven't yet been through menopause. Approved AIs include letrozole (Femara), anastrozole (Arimidex) and exemestane (Aromasin). (3) Luteinizing hormone-releasing hormone (LH-RH) agonists and antagonists—LH-RH agonists—sometimes called analogs —and LH-RH antagonists reduce the level of hormones by altering the mechanisms in the brain that tell the body to produce hormones. LH-RH agonists are essentially a chemical alternative to surgery for removal of the ovaries for women, or of the testicles for men. Depending on the cancer type, one might choose this route if they hope to have children in the future and want to avoid surgical castration. In most cases the effects of these drugs are reversible. Examples of LH-RH agonists include: Leuprolide (Lupron, Viadur, Eligard) for prostate cancer, Goserelin (Zoladex) for breast and prostate cancers, Triptorelin (Trelstar) for ovarian and prostate cancers and abarelix (Plenaxis).

One class of pharmaceuticals is the Selective Estrogen Receptor Modulators or SERMs. SERMs block the action of estrogen in the breast and certain other tissues by occupying estrogen receptors inside cells. SERMs include, but are not limited to tamoxifen (the brand name is Nolvadex, generic tamoxifen citrate); Raloxifene (brand name: Evista), and toremifene (brand name: Fareston).

VI. Kits

Further embodiments of the invention include kits for the measurement, analysis, and reporting of gene expression and transcriptional output. A kit may include, but is not limited to microarray, quantitative RT-PCR, antibodies, labeling or other reagents and materials, as well as hardware and/or software for performing at least a portion of the methods described. For example, custom microarrays or analysis methods for existing microarrays are contemplated. Also, methods of the invention include methods of accessing and using a reporting system that compares a single result to a scale of clinical trial results. In yet still further aspects of the invention, a digital standard for data normalization is contemplated so that the assay result values from future samples would be able to be directly compared with the assay value results from past samples, such as from specific clinical trials.

EXAMPLES

The following examples are given for the purpose of illustrating various embodiments of the invention and are not meant to limit the present invention in any fashion. One skilled in the art will appreciate readily that the present invention is well adapted to carry out the objects and obtain the ends and advantages mentioned, as well as those objects, ends and advantages inherent herein. The present examples, along with the methods described herein are presently representative of preferred embodiments, are exemplary, and are not intended as limitations on the scope of the invention. Changes therein and other uses which are encompassed within the spirit of the invention as defined by the scope of the claims will occur to those skilled in the art.

Example 1 Materials and Methods

Needle biopsy samples (fine needle aspirates—FNAs or core biopsies—CBX) were analyzed in order to examine genes correlated with the selected endpoint. The genes were identified by this method using these samples and methods to standardize data were done in order to facilitate calculation of the predictor indices consistently in different sample types such as biopsies, resected tissue from an excised tumor, and frozen tumor tissue.

Patients and samples—Patients prospectively consented to an Institutional Research Board approved research protocol (LAB99-402, USO-02-103, 2003-0321, I-SPY-1) to obtain a tumor biopsy by fine needle aspiration (FNA) or core biopsy (CBX) prior to any systemic therapy for genomic studies to develop and test predictors of treatment outcome. Clinical nodal status was determined before treatment from physical examination, with or without axillary ultrasound, with diagnostic FNA as required. Pathologic HER2 status was defined as negative according to the ASCO/CAP guidelines. Patients with any nuclear immunostaining for ER in the tumor cells were considered as eligible for adjuvant endocrine therapy. During this research, patients were consented to undergo pretreatment biopsy as fine needle aspiration (FNA) (Ayers, 2004; Hess, 2006) or core needle biopsy, of the primary breast tumor or ipsilateral axillary metastasis before starting chemotherapy as part of an ongoing pharmacogenomic marker discovery program. Gene expression data generated from the biopsies captures the molecular characteristics of the invasive cancer including the molecular class (Pusztai, 2003). At least 70% of all aspirations yielded at least 1 μg total RNA that is required for the gene expression profiling. The main reason for failure to obtain sufficient RNA was acellular aspirations. Three hundred and ten (310) patients with at least 1 μg RNA were included in this analysis. All patients received neoadjuvant chemotherapy consisting of a combination of either paclitaxel or docetaxel with anthracycline. At the completion of neoadjuvant chemotherapy all patients had modified radical mastectomy or lumpectomy and sentinel lymph node biopsy or axillary node dissection as determined appropriate by the surgeon. Patients who were ER-positive also received endocrine therapy as tamoxifen or aromatase inhibitor. Clinical characteristics of the patients are in Table 1A.

-   Discovery of predictor of relapse after therapy: Table 1B describes     the breakdown of samples between FNAs and core biopsies and the     treatments administered to the patients. Validation of predictors of     response and relapse after therapy: Table 1A and 1B also describe     the patients whose samples were used to validate the predictors     developed for outcome of chemotherapy. Patient samples were     collected at University of Texas M. D. Anderson Cancer Center     (MDACC), LBJ Hospital, and US Oncology, in Houston, Tex. and at     cancer centers in Peru, Mexico and Spain. During this research,     patients were consented to undergo pretreatment biopsy as fine     needle aspiration (FNA) (Ayers, 2004; Hess, 2006) or core needle     biopsy, of the primary breast tumor or ipsilateral axillary     metastasis before starting chemotherapy as part of an ongoing     pharmacogenomic marker discovery program. One hundred and ninety     eight (198) patients with at least 1 μg RNA and data on relapse-free     survival to perform survival analysis were included in this     analysis. All patients received either neoadjuvant chemotherapy, or     in a small group, adjuvant chemotherapy, consisting of a combination     of either paclitaxel or docetaxel with anthracycline. At the     completion of neoadjuvant chemotherapy all patients had modified     radical mastectomy or lumpectomy and sentinel lymph node biopsy or     axillary node dissection as determined appropriate by the surgeon.     Patients who were ER-positive also received endocrine therapy as     tamoxifen or aromatase inhibitor. This study was approved by the     institutional review boards (IRB) of the respective institutions and     all patients signed an informed consent for voluntary participation.

TABLE 1A Patient characteristics in development and validation of the predictors Discovery Population Validation Population MDACC^(a) I-SPY^(b) Total MDACC LBJ^(c)/IN^(d)/GEI^(e) USO^(f) Total Patients Age 227  83  310 86  58  54  198  <=50 112 (49%) 30 (36%) 142 (46%) 48 (56%) 30 (52%) 31 (57%) 109 (55%) >50 115 (51%) 53 (64%) 168 (54%) 38 (44%) 28 (48%) 23 (43%) 89 (45%) Mean (SD) 51 (11) 47 (8) 50 (10) 49 (11) 51 (11) 48 (9) 49 (11) Nodal status Pos 165 (73%) 58 (70%) 223 (72%) 52 (60%) 42 (72%) 34 (63%) 128 (65%) Neg 62 (27%) 25 (30%) 87 (28%) 34 (40%) 16 (28%) 20 (37%) 70 (35%) T stage 0 2 (1%) 0 2 (1%) 1 (1%) 0 0 1 (1%) 1 19 (8%) 1 (1%) 20 (6%) 8 (9%) 1 (1%) 1 (2%) 10 (5%) 2 131 (58%) 34 (41%) 165 (53%) 52 (61%) 19 (33%) 19 (35%) 90 (45%) 3 35 (15%) 39 (47%) 74 (24%) 18 (21%) 19 (33%) 34 (63%) 71 (36%) 4 40 (18%) 9 (11%) 49 (16%) 7 (8%) 19 (33%) 0 26 (13%) Grade 1 13 (6%) 6 (7%) 19 (6%) 7 (8%) 5 (8%) 1 (2%) 13 (7%) 2 92 (40%) 25 (30%) 117 (38%) 28 (33%) 19 (33%) 16 (30%) 63 (32%) 3 122 (54%) 29 (35%) 151 (49%) 51 (59%) 23 (40%) 34 (63%) 108 (54%) Unknown 0 23 (28%) 23 (7%) 0 11 (19%) 3 (5%) 14 (7%) AJCC^(g) Stage I 6 (3%) 0 6 (2%) 2 (2%) 0 0 2 (1%) II 126 (55%) 39 (47%) 165 (53%) 57 66%) 18 (31%) 32 (59%) 107 (54%) III 95 (42%) 44 (53%) 139 (45%) 27 (32%) 40 (69%) 22 (41%) 89 (45%) ER^(h) Status Pos 131 (58%) 43 (52%) 174 (56%) 60 (70%) 37 (64%) 27 (50%) 124 (63%) Neg 96 (42%) 35 (42%) 131 (42%) 26 (30%) 21 (36%) 27 (50%) 74 (37%) Indeterminate 0 5 (6%) 5 (2%) 0 0 0 0 PR^(i) Status Pos 102 (45%) 40 (48%) 142 (46%) 43 (50%) 31 (53%) 28 (52%) 102 (52%) Neg 125 (55%) 37 (45%) 162 (52%) 43 (50%) 27 (47%) 26 (48%) 96 (48%) Indeterminate 0 6 (7%) 6 (2%) 0 0 0 0 ^(a)M. D. Anderson Cancer Center; ^(b)I-SPY-1 clinical trial; ^(c)Lyndon B. Johnson Hospital; ^(d)Instituto Nacional de Enfermedades Neoplásicas (INEN); ^(e)Grupo Español de Investigación en Cáncer de Mama (GEICAM); ^(f)US Oncology; ^(g)American Joint Committee on Cancer; ^(h)Estrogen receptor; ^(i)Progesterone receptor.

TABLE 1B Chemotherapy And Pre-treatment Biopsy Details for the Study Cohorts Discovery Validation Cohort Cohort (N = 310) (N = 198) Needle Biopsy for Genomic Testing FNA 227 157 CBX 83 41 Chemotherapy Regimen Entirely Neoadjuvant T × 12 → FAC × 4 → Sx¹ 227 73 AC × 4 → T/Tx × 4 → Sx² 83 — TxX × 4 → FEC × 4 → Sx³ — 92 Partial Neoadjuvant FAC/FEC × 6 → Sx → T × 12⁴ — 18 Entirely Adjuvant Sx → T × 12 → FAC/FEC × 4⁵ — 12 Sx → TxX × 4 → FEC × 4⁶ — 2 Sx → Tx × 4 → FEC × 4⁷ — 1 FNA: fine needle aspiration CBX: core needle biopsy Sx: surgery ¹12 weekly doses of paclitaxel (T) followed by four cycles of fluorouracil (F), doxorubicin (A) and cyclophosphamide (C) and then surgery. ²Four cycles of doxorubicin (A) and cyclophosphamide (C) followed by four cycles of paclitaxel (T) (N = 60) or docetaxel (Tx) (N = 18) or taxane not specified (N = 5) and then surgery. ³Four cycles of docetaxel (Tx) with capecitabine (X) followed by four cycles of fluorouracil (F), epirubicin (E) and cyclophosphamide (C) and then surgery. ⁴Six cycles of fluorouracil (F), doxorubicin (A) or epirubicin (E), and cyclophosphamide (C) followed by surgery and then by 12 weekly doses of paclitaxel (T). ⁵Surgery followed by 12 weekly doses of paclitaxel (T) and then by four cycles of fluorouracil (F), doxorubicin (A) or epirubicin (E), and cyclophosphamide (C). ⁶Surgery followed by four cycles of docetaxel (Tx) with capecitabine (X) and then followed by four cycles of fluorouracil (F), epirubicin (E) and cyclophosphamide (C). ⁷Surgery followed by four cycles of docetaxel (Tx) and then by four cycles of fluorouracil (F), epirubicin (E) and cyclophosphamide (C).

RNA extraction and gene expression profiling—Biopsy samples were either collected in 1.5 ml RNAlater™ (Qiagen, Valencia, Calif.) and stored locally at −70° C. and transported to the laboratory on dry ice (MDACC, INEN, LBJ, GEICAM) or couriered overnight in a cooler pack from clinics to the laboratory (USO), or were frozen, cryosectioned and an aliquot of RNA sent to the laboratory on dry ice (I-SPY). Details of our methods for RNA purification and microarray hybridization have been reported previously Rouzier, 2005; Stec, 2005; Symmans, 2003). Briefly, a single-round T7 amplification was used to generate biotin-labeled cRNA for hybridization to oligonucleotide microarrays (U133A GeneChip™, Affymetrix, Santa Clara, Calif.). Gene expression levels were derived from multiple oligonucleotide probes on the microarray that hybridize to different sequence sites of a gene transcript (probe sets).

Microarray quality control—Quality control (QC) checks are performed at 3 levels (i) RNA yield, (ii) cRNA yield, and (ii) chip hybridization signal) and samples that fail at any level are not processed further. The amount and quality of RNA is assessed with NanoDrop ND-1000 Spectrophotometer (Thermo Fisher scientific In, Wilmington, Del., USA) and is generally considered adequate for further analysis if the OD 260/280 ratio is between 1.8-2.1 and the total RNA yield is ≧1.0 microgram. If total RNA yield is <1.0 microgram all remaining samples (if available) from that patient are used for RNA extraction. At least 10 μg of biotin-labeled cRNA need to be generated from a single-round in vitro transcription protocol to proceed with hybridized to U133A chips.

Microarray data normalization—Raw intensity files (.CEL) from each microarray were processed using MAS5.0 (R/Bioconductor, www.bioconductor.org)¹ to normalize to a mean array intensity of 600 and to generate probe set-level expression values. Expression values were then log2-transformed and subsequently scaled by the expression levels of 1322 breast cancer reference genes to reference values that had been established as the median expression of these genes in an independent reference cohort of invasive breast cancer (N=444). The quality of hybridization and microarray profiling was assessed based on a set of 8 metrics that compare the expression level of the reference genes in each sample to the historical reference values before and after scaling. Metrics include the median deviation, the inter-quartile range (IQR) of deviations, the Kolmogorov-Smirnov statistic for equality of the distributions and the p-value of the K-S statistic. Dimensionality was reduced through a principal component analysis (PCA) model of the 8 metrics which were further summarized in two multivariate statistics, the Hotteling T2 and the sum of squares of the residuals or Q statistic (Jackson & Mudholkar, 1979). Control limits for Q and T2 for sample acceptance were established from historical in-control samples. Prior to analysis for predictor development, 2,522 probe sets that either had low specificity (extensions _xfri_ in their name), were housekeeping probes (starting with AFFX) or were not adequately expressed (log2-transformed intensity of at least 5 in at least 75% of the arrays) were removed. A total of 16,289 probe sets (73% of all) were retained for further analysis.

Example 2 Predictor of Distant Relapse After Therapy or of Resistance to Therapy

Methods for building predictor of survival outcomes as a result of therapy—Distant relapse-free survival (DRFS) was used as the endpoint of favorable outcome of therapy to build the predictor genes. Prior to analysis, probes that either had low specificity (those that include extensions _xfri_ in their name) or housekeeping probes (those starting with AFFX) were selected and removed from the candidate probesets. This process removed 2522 probesets. Subsequently, a non-specific filter was applied to retain probesets that has log2-transformed intensity of at least 5 in at least 75% of the arrays. A total of 16289 probesets (73% of all) were retained for further analysis.

The samples in the development cohort were subdivided in ER+ and ER− subsets and in lymph node negative (N0) and lymph positive (NP) subsets within each ER group. Means and standard deviations (SDs) of the 16289 genes were computed for each of the 4 subsets of cases. Within each ER cohort, the means and SDs for N0 and NP subsets were averaged to yield nodal-status adjusted statistics. These means and SDs were then used to scale the expression values of all probesets using the corresponding statistics for ER+ or ER− cases.

Each probeset was evaluated in a univariate Cox regression model for the significance of its association with risk of distant relapse. For this analysis, distant relapses or breast-cancer related deaths were considered as events, whereas local relapses were censored at the time of occurrence. Time to event was determined since the time of initial diagnosis. The significance of the association of each probeset to distant relapse risk was assessed based on the likelihood ratio test, which compares the log-likelihood of the model having the given probeset as the only covariate to the null model. The likelihood ratio statistic is distributed according to a chi-squared with one degree of freedom. P-values for the significance of each probeset were calculated from this distribution.

To account for sampling variability in the training dataset, Cox regression models for each probeset were fit repeatedly using a bootstrap procedure in which cases were sampled with replacement to generate bootstrapped datasets of the same size as the original dataset. This process was repeated 499 times, thus generating 500 estimates for the p-values of each probeset. The association of each probeset with distant relapse risk was assessed within each bootstrapped dataset at a critical significance level of 0.001 or 0.0005 to account for multiple testing. Those probesets that were called significant in at least 20% of the bootstrap replicates were selected as candidate probesets. This process was applied separately to the

ER-positive and ER-negative cases in the training dataset and resulted in 235 and 268 candidate probesets in the ER+ and ER− subsets.

Final multivariate prediction models were built from the candidate probesets in the ER+ and ER− cohorts. Maximization of the partial likelihood associated with Cox proportional hazards models becomes problematic and non-unique if the number of covariates exceeds the number of available samples or if there is a high degree of colinearity between the predictors. To prevent this pathologic behavior, some sort of regularization or shrinkage needs to be applied to the regression coefficients to allow efficient estimation of the remaining ones. The Cox univariate shrinkage (CUS) approach was used for this purpose (Tibshirani, 2009), which is equivalent to the lasso estimate in standard regression analysis. The level of penalization is an adjustable parameter in the algorithm, with higher penalization resulting in smaller signatures. The optimal level of penalization was determined under 5-fold cross-validation as the penalization level that resulted in the shortest list of genes that yielded the highest incremental improvement in the Cox model's deviance.

The final predictors for ER+ and ER− subsets used 33 probesets and 27 probesets respectively to make the predictions. The probesets, genes that they encode for, and their weights (Cox coefficients) are shown in Table 2. The risk score is calculated by multiplying the scaled log2-transformed expression level of each gene in a given sample by its corresponding weight and then adding up the weighted expression values for all genes in the signature. The following formula describes the score calculation for sample i:

$y_{i} = \left\{ \begin{matrix} {{\sum\limits_{j = 1}^{K +}{w_{j}^{+}z_{ij}^{+}}},} & {{if}\mspace{14mu} {ER}\mspace{14mu} {positive}} \\ {{\sum\limits_{j = 1}^{K -}{w_{j}^{-}z_{ij}^{-}}},} & {{if}\mspace{14mu} {ER}\mspace{14mu} {negative}} \end{matrix} \right.$

-   where w_(j) is the weight of gene j in the signature, z_(ij) is the     log2-transformed and scaled expression value of gene j in sample i,     K is the number of genes in the signature, and the + or − symbols     refer to the ER+ and ER− signatures.

A cut point was selected to dichotomize the risk score and predict two risk classes. The optimal cutoff was selected in order to maximize the accuracy of the prediction of 5-yr distant relapse outcome by the risk classes. A cutoff of 0 was selected for both the ER+ and ER− scores. Positive scores signify “High risk” class, i.e. higher risk of distant relapse and a zero or negative score signifies “Low risk”.

TABLE 2 Genes used for prediction of distant relapse risk in ER-stratified patient subsets Probe Set Symbol Description GeneID Chromosome Cytoband Weight ER-Positive 1 212174_at AK2 adenylate kinase 2 204 1 1p34 0.0011 2 215407_s_at ASTN2 astrotactin 2 23245 9 9q33.1 −0.0131 3 205626_s_at CALB1 calbindin 1, 28 kDa 793 8 8q21.3-q22.1 0.008 4 212816_s_at CBS cystathionine-beta- 875 21 21q22.3 0.0116 synthase 5 216923_at CDLK5 cyclin-dependent kinase- 6792 X Xp22.13 −0.0084 like 5 6 205471_s_at DACH1 dachshund homolog 1 1602 13 13q22 −0.0043 (Drosophila) 7 221681_s_at DSPP dentin 1834 4 4q21.3 −0.0285 sialophosphoprotein 8 201539_s_at FHL1 four and a half LIM 2273 X Xq26 0.0142 domains 1 9 215744_at FUS fusion (involved in t(12; 16) 2521 16 16p11.2 −0.0016 in malignant liposarcoma) 10 209604_s_at GATA3 GATA binding protein 3 2625 10 10p15 −0.0414 11 209602_s_at GATA3 GATA binding protein 3 2625 10 10p15 −0.0285 12 209603_at GATA3 GATA binding protein 3 2625 10 10p15 −0.0067 13 203821_at HBEGF heparin-binding EGF-like 1839 5 5q23 −0.0126 growth factor 14 219976_at HOOK1 hook homolog 1 51361 1 1p32.1 −0.0136 (Drosophila) 15 212531_at LCN2 lipocalin 2 3934 9 9q34 0.0411 16 220906_at LDB2 LIM domain binding 2 9079 4 p15.32 −0.0358 17 217506_at LOC339290 hypothetical LOC339290 339290 18 18p11.31 −0.0171 18 204058_at ME1 malic enzyme 1, 4199 6 6q12 0.0002 NADP(+)-dependent, cytosolic 19 200899_s_at MGEA5 meningioma expressed 10724 10 10q24.1-q24.3 −0.0023 antigen 5 (hyaluronidase) 20 203419_at MLL4 myeloid/lymphoid or 9757 19 19q13.1 −0.0097 mixed-lineage leukemia 4 21 211874_s_at MYST4 MYST histone 23522 10 10q22.2 −0.0336 acetyltransferase (monocytic leukemia) 4 22 40569_at MZF1 myeloid zinc finger 1 7593 19 19q13.4 −0.0349 23 203621_at NDUFB5 NADH dehydrogenase 4711 3 3q26.33 0.0448 (ubiquinone) 1 beta subcomplex, 5, 16 kDa 24 202886_s_at PPP2R1B protein phosphatase 2 5519 11 11q23.2 0.0061 (formerly 2A), regulatory subunit A, beta isoform 25 201834_at PRKAB1 protein kinase, AMP- 5564 12 12q24.1 −0.0341 activated, beta 1 non- catalytic subunit 26 212743_at RCHY1 ring finger and CHY zinc 25898 4 4q21.1 −0.0127 finger domain containing 1 27 219869_s_at SLC39A8 solute carrier family 39 64116 4 4q22-q24 0.0262 (zinc transporter), member 8 28 210692_s_at SLC43A3 solute carrier family 43, 29015 11 11q11 0.0075 member 3 29 213103_at STARD13 StAR-related lipid transfer 90627 13 13q12-q13 −0.0185 (START) domain containing 13 30 202342_s_at TRIM2 tripartite motif-containing 2 23321 4 4q31.3 0.0088 31 212534_at ZNF24 zinc finger protein 24 7572 18 18q12 −0.0025 32 219635_at ZNF606 zinc finger protein 606 80095 19 19q13.4 −0.0198 33 214202_at — — — 5 5q22.3 −0.0421 ER-Negative 1 200982_s_at ANXA6 annexin A6 309 5 5q32-q34 0.0136 2 212136_at ATP2B4 ATPase, Ca++ transporting, plasma membrane 493 1 1q32.1 0.0123 4 3 205379_at CBR3 carbonyl reductase 3 874 21 21q22.2 −0.0067 4 219755_at CBX8 chromobox homolog 8 (Pc class homolog, 57332 17 17q25.3 −0.0023 Drosophila) 5 204720_s_at DNAJC6 DnaJ (Hsp40) homolog, subfamily C, member 9829 1 1pter-q31.3 0.0022 6 6 203303_at DYNLT3 dynein, light chain, Tctex-type 3 6990 X Xp21 0.0041 7 216682_s_at FAM48A family with sequence similarity 48, member A 55578 13 13q13.3 0.0044 8 206847_s_at HOXA7 homeobox A7 3204 7 7p15-p14 −0.0323 9 219284_at HSPBAP1 HSPB (heat shock 27 kDa) associated protein 1 79663 3 3q21.1 0.0068 10 210036_s_at KCNH2 potassium voltage-gated channel, subfamily H 3757 7 7q35-q36 0.0158 (eag-related), member 2 11 217929_s_at KIAA0319L KIAA0319-like 79932 1 1p34.2 −0.0044 12 201932_at LRRC41 leucine rich repeat containing 41 10489 1 1p34.1 −0.0089 13 205301_s_at OGG1 8-oxoguanine DNA glycosylase 4968 3 3p26.2 −0.0025 14 208393_s_at RAD50 RAD50 homolog (S. cerevisiae) 10111 5 5q31 0.0404 15 203286_at RNF44 ring finger protein 44 22838 5 5q35.2 0.0061 16 213044_at ROCK1 Rho-associated, coiled-coil containing protein 6093 18 18q11.1 0.0138 kinase 1 17 203889_at SCG5 secretogranin V (7B2 protein) 6447 15 15q13-q14 0.0065 18 221053_s_at TDRKH tudor and KH domain containing 11022 1 1q21 0.0107 19 203254_s_at TLN1 talin 1 7094 9 9p13 0.0167 20 210180_s_at TRA2B transformer 2 beta homolog (Drosophila) 6434 3 3q26.2-q27 −0.001 21 221836_s_at TRAPPC9 trafficking protein particle complex 9 83696 8 8q24.3 0.0165 22 208349_at TRPA1 transient receptor potential cation channel, 8989 8 8q13 0.025 subfamily A, member 1 23 216374_at TSPY1 testis specific protein, Y-linked 1 7258 Y Yp11.2 0.0079 24 218715_at UTP6 UTP6, small subunit (SSU) processome 55813 17 17q11.2 0.0142 component, homolog (yeast) 25 208453_s_at XPNPEP1 X-prolyl aminopeptidase (aminopeptidase P) 1, 7511 10 10q25.3 −0.0208 soluble 26 214900_at ZKSCAN1 zinc finger with KRAB and SCAN domains 1 7586 7 7q21.3-q22.1 −0.0032 27 215298_at — — — 4 4q8.3 0.0039

Example 3 Performance of Relapse-Based Predictor in Chemotherapy Outcomes Prediction

FIG. 1 shows the survival outcome of patients from the validation cohort (Table 1A) predicted as good and poor responders by the ER-stratified outcomes predictor described in Example 2. Survival is defined by distant relapse-free survival (DRFS) over a period of about 60 months since the initial biopsy. These patients have undergone surgery where it was considered appropriate and the ER-positive patients received hormonal therapy (tamoxifen or aromatase inhibitor) for 5 years after the surgery. ER-negative patients did not receive any additional treatment post-surgery.

The plot shows that predicted good and poor responders to taxane-chemotherapy (FIG. 1) have distinctly separated relapse-free survival curves (p=0.008). The good responders (51%) or “low-risk” patients show a fewer number of distant relapse events (˜85% relapse-free after 60 months) whereas the remaining patients show considerably higher relapse rates among the patients (˜60% DRFS after 60 months).

Example 4 Predictor of Response to Chemotherapy

Patients and samples—Patient samples used were those shown in Table 1A. All other laboratory analytic methods were the same as in Example 1.

Methods for building predictors of response to chemotherapy—The inventors used the response endpoint RCB0/I, representing no residual disease or minimal residual disease measured at the completion of neoadjuvant chemotherapy, to identify genes that differentiated patients who responded to chemotherapy versus all others in the discovery cohort of Table 1A. Prior to analysis, probes that either had low specificity (those that include extensions _xfri_ in their name) or housekeeping probes (those starting with AFFX) were selected and removed from the candidate probesets. This process removed 2522 probesets. Subsequently, a non-specific filter was applied to retain probesets that has log2-transformed intensity of at least 5 in at least 75% of the arrays. A total of 16289 probesets (73% of all) were retained for further analysis.

The samples in the development cohort were subdivided in ER+ and ER− subsets and in lymph node negative (N0) and lymph positive (NP) subsets within each ER group. Means and standard deviations (SDs) of the 16289 genes were computed for each of the 4 subsets of cases. Within each ER cohort, the means and SDs for N0 and NP subsets were averaged to yield nodal-status adjusted statistics. These means and SDs were then used to scale the expression values of all probesets using the corresponding statistics for ER+ or ER− cases.

Each probeset was evaluated for differential expression in the two responder groups (RCB-0/I vs rest) using an unequal variance t-statistic based on the trimmed means and trimmed standard deviations in the two groups using a trim fraction of 0.025 (i.e. the lowest 2.5% and highest 2.5% values were eliminated and the statistics were calculated on the remaining 95% of the observations in each group). Degrees of freedom for the unequal variance t-statistic were estimated based on Satterthwaite's approximation (Armitage, Berry & Matthews, 2002). The significance of association of each probe set with response was assessed based on the unequal variance t-statistic. P-values for the significance of each probeset were calculated from the t-distribution with the corresponding degrees of freedom.

To account for sampling variability in the training dataset, the differential expression analysis for each probeset described in the previous paragraph was performed repeatedly using a bootstrap procedure in which cases were sampled with replacement to generate bootstrapped datasets of the same size as the original dataset. This process was repeated 499 times, thus generating 500 estimates for the p-values of each probeset. The association of each probeset with distant relapse risk was assessed within each bootstrapped dataset at a critical significance level of 0.0005 to account for multiple testing. Those probesets that were called significant in at least 30% of the bootstrap replicates were selected as candidate probesets. This process was applied separately to the ER-positive and ER-negative cases in the training dataset and resulted in 209 and 244 candidate probesets in the ER+ and ER− subsets.

In developing the RCB-based chemotherapy response predictor, the inventors used an approach that combines feature selection and model discovery using a multivariate penalized approach called Gradient Directed Regularization developed by Prof. J. Friedman at Stanford University, a description of which can be found on the World Wide Web at stat.stanford.edu/˜jhf/ftp/pathlite.pdf. The informative genes are selected through penalization using the maximization of the area under the ROC curve (AUC) as the optimization criterion. Ma and Huang have previously used a similar approach for disease classification (Ma, 2006).

For predictor discovery and evaluation the inventors followed a cross-validation protocol. First, the input dataset is randomly partitioned into a training set and a test set. A 5-fold cross-validation for a 4:1 split stratified by response group between training and test sets was used (Dudoit, 2002). The training set consisting of ⅘ of the original data is used to develop the predictor. The algorithm starts with the same initial list of candidate genes that were determined through the bootstrap procedure and iteratively refines the predictor by selecting genes that contribute in maximizing the AUC of the candidate predictor. The maximum level of penalization is used to derive the most parsimonious predictors. Since different optimal reporter gene sets might result from the different internal cross-validation folds, the number of times each gene is selected is tracked to provide a measure of its importance or its reliability. The trained predictor is then tested on the ⅕ hold-out part of the training dataset and its performance is evaluated based on the AUC.

The entire process of randomly splitting the data to a training- and a test-set was repeated 499 times to obtain the distributions and summary statistics of the performance metrics from the cross-validated replicates.

The final predictors for ER+ and ER− subsets used 39 probesets and 55 probesets respectively to make the predictions. The probesets, genes that they encode for, and their weights (coefficients) are shown in Table 3. The risk score is calculated by multiplying the scaled log2-transformed expression level of each gene in a given sample by its corresponding weight and then adding up the weighted expression values for all genes in the signature. The following formula describes the score calculation for sample i:

$y_{i} = \left\{ \begin{matrix} {{\sum\limits_{j = 1}^{K +}{w_{j}^{+}z_{ij}^{+}}},} & {{if}\mspace{14mu} {ER}\mspace{14mu} {positive}} \\ {{\sum\limits_{j = 1}^{K -}{w_{j}^{-}z_{ij}^{-}}},} & {{if}\mspace{14mu} {ER}\mspace{14mu} {negative}} \end{matrix} \right.$

-   where w_(j) is the weight of gene j in the signature, z_(ij) is the     log2-transformed and scaled expression value of gene j in sample i,     K is the number of genes in the signature, and the + or − symbols     refer to the ER+ and ER− signatures.

A cut point was selected to dichotomize the risk score and predict two risk classes. The optimal cutoff was selected in order to maximize the accuracy of the prediction. A cutoff of 0 was selected for both the ER+ and ER− scores. Positive scores signify “responders” and a zero or negative score signifies “non-responders”.

TABLE 3 Genes used for prediction of response, RCB-0/1, in ER-stratified patient subsets Probe Set Symbol Description GeneID Chromosome Cytoband Weight ER-Positive 1 204332_s_at AGA aspartylglucosaminidase 175 4 4q32-q33 1.023626 2 36865_at ANGEL1 angel homolog 1 23357 14 14q24.3 0.538063 (Drosophila) 3 219437_s_at ANKRD11 ankyrin repeat domain 29123 16 16q24.3 0.26952 11 4 205865_at ARID3A AT rich interactive 1820 19 19p13.3 0.832093 domain 3A (BRIGHT- like) 5 215407_s_at ASTN2 astrotactin 2 23245 9 9q33.1 1.081851 6 204493_at BID BH3 interacting domain 637 22 22q11.1 0.351295 death agonist 7 205557_at BPI bactericidal/permeability- 671 20 20q11.23-q12 −1.05657 increasing protein 8 42361_g_at CCHCR1 coiled-coil alpha-helical 54535 6 6p21.3 −0.19308 rod protein 1 9 205937_at CGREF1 cell growth regulator 10669 2 2p23.3 0.616448 with EF-hand domain 1 10 208817_at COMT catechol-O- 1312 22 22q11.21 0.964167 methyltransferase 11 202250_s_at DCAF8 DDB1 and CUL4 50717 1 1q22-q23 0.438059 associated factor 8 12 202570_s_at DLGAP4 discs, large (Drosophila) 22839 20 20q11.23 −0.03735 homolog-associated protein 4 13 218103_at FTSJ3 FtsJ homolog 3 (E. coli) 117246 17 17q23.3 0.902969 14 216651_s_at GAD2 glutamate 2572 10 10p11.23 1.191928 decarboxylase 2 (pancreatic islets and brain, 65 kDa) 15 205505_at GCNT1 glucosaminyl (N-acetyl) 2650 9 9q13 0.635989 transferase 1, core 2 (beta-1,6-N- acetylglucosaminyl transferase) 16 213020_at GOSR1 golgi SNAP receptor 9527 17 17q11 0.041002 complex member 1 17 212597_s_at HMGXB4 HMG box domain 10042 22 22q13.1 0.241141 containing 4 18 212898_at KIAA0406 KIAA0406 9675 20 20q11.23 −0.37731 19 220652_at KIF24 kinesin family member 347240 9 9p13.3 −0.85991 24 20 218486_at KLF11 Kruppel-like factor 11 8462 2 2p25 0.145703 21 202057_at KPNA1 karyopherin alpha 1 3836 3 3q21 0.047619 (importin alpha 5) 22 209204_at LMO4 LIM domain only 4 8543 1 1p22.3 0.906757 23 201818_at LPCAT1 lysophosphatidylcholine 79888 5 5p15.33 0.602505 acyltransferase 1 24 208328_s_at MEF2A myocyte enhancer 4205 15 15q26 0.196532 factor 2A 25 215491_at MYCL1 v-myc 4610 1 1p34.2 1.199616 myelocytomatosis viral oncogene homolog 1, lung carcinoma derived (avian) 26 202944_at NAGA N- 4668 22 22q11 0.053596 acetylgalactosaminidase, alpha- 27 218886_at PAK1IP1 PAK1 interacting protein 55003 6 6p24.2 −0.39992 1 28 207081_s_at PI4KA phosphatidylinositol 4- 5297 22 22q11.21 0.879705 kinase, catalytic, alpha 29 210771_at PPARA peroxisome proliferator- 5465 22 22q12-q13.1 0.771244 activated receptor alpha 30 203096_s_at RAPGEF2 Rap guanine nucleotide 9693 4 4q32.1 0.645585 exchange factor (GEF) 2 31 218593_at RBM28 RNA binding motif 55131 7 7q32.1 0.533325 protein 28 32 211678_s_at RNF114 ring finger protein 114 55905 20 20q13.13 1.178185 33 202762_at ROCK2 Rho-associated, coiled- 9475 2 2p24 1 coil containing protein kinase 2 34 206239_s_at SPINK1 serine peptidase 6690 5 5q32 0.620242 inhibitor, Kazal type 1 35 221276_s_at SYNC syncoilin, intermediate 81493 1 1p34.3-p33 −0.38482 filament protein 36 213155_at WSCD1 WSC domain containing 23302 17 17p13.2 −0.31573 1 37 37117_at PRR5 proline rich 5 (renal) 55615 22 22q13 0.106363 38 220855_at AC091271.1 no-protein transcript — 17 17q23.2 −0.3595 39 222275_at — — — 5 5p12 0.03155 ER-Negative 1 202442_at AP3S1 adaptor-related protein 1176 5 5q22 −0.19044 complex 3, sigma 1 subunit 2 212135_s_at ATP2B4 ATPase, Ca++ 493 1 1q32.1 −0.3245 transporting, plasma membrane 4 3 217911_s_at BAG3 BCL2-associated 9531 10 10q25.2-q26.2 −0.23225 athanogene 3 4 210214_s_at BMPR2 bone morphogenetic 659 2 2q33-q34 0.814841 protein receptor, type II (serine/threonine kinase) 5 202048_s_at CBX6 chromobox homolog 6 23466 22 22q13.1 −1.02907 6 203653_s_at COIL coilin 8161 17 17q22-q23 0.078687 7 203633_at CPT1A carnitine 1374 11 11q13.1-q13.2 −0.06407 palmitoyltransferase 1A (liver) 8 210096_at CYP4B1 cytochrome P450, family 1580 1 1p34-p12 −0.39651 4, subfamily B, polypeptide 1 9 212838_at DNMBP dynamin binding protein 23268 10 10q24.2 −0.07158 10 219850_s_at EHF ets homologous factor 26298 11 11p12 0.115972 11 201936_s_at EIF4G3 eukaryotic translation 8672 1 1p36.12 −0.08341 initiation factor 4 gamma, 3 12 217254_s_at EPO erythropoietin 2056 7 7q22 −0.9403 13 205774_at F12 coagulation factor XII 2161 5 5q33-qter −0.21253 (Hageman factor) 14 218532_s_at FAM134B family with sequence 54463 5 5p15.1 −0.12462 similarity 134, member B 15 200709_at FKBP1A FK506 binding protein 2280 20 20p13 −0.06741 1A, 12 kDa 16 212294_at GNG12 guanine nucleotide 55970 1 1p31.3 −0.2595 binding protein (G protein), gamma 12 17 211525_s_at GP5 glycoprotein V (platelet) 2814 3 3q29 −0.52858 18 212090_at GRINA glutamate receptor, 2907 8 8q24.3 −0.02213 ionotropic, N-methyl D- aspartate-associated protein 1 (glutamate binding) 19 213053_at HAUS5 HAUS augmin-like 23354 19 19q13.12 0.395212 complex, subunit 5 20 214537_at HIST1H1D histone cluster 1, H1d 3007 6 6p21.3 0.029003 21 206194_at HOXC4 homeobox C4 3221 12 12q13.3 −0.10183 22 204544_at HPS5 Hermansky-Pudlak 11234 11 11p14 0.203156 syndrome 5 23 205700_at HSD17B6 hydroxysteroid (17-beta) 8630 12 12q13 −0.88741 dehydrogenase 6 homolog (mouse) 24 209575_at IL10RB interleukin 10 receptor, 3588 21 21q22.1-q22.2 0.162807 beta 25 215177_s_at ITGA6 integrin, alpha 6 3655 2 2q31.1 0.34206 26 221986_s_at KLHL24 kelch-like 24 (Drosophila) 54800 3 3q27.1 1 27 208107_s_at LOC81691 exonuclease NEF-sp 81691 16 16p12.3 0.618062 28 221650_s_at MED18 mediator complex 54797 1 1p35.3 −0.05596 subunit 18 29 218251_at MID1IP1 MID1 interacting protein 58526 X Xp11.4 −0.41753 1 (gastrulation specific G12 homolog (zebrafish)) 30 215563_s_at MSTP9 macrophage stimulating, 11223 1 1p36.13 −0.02463 pseudogene 9 31 221207_s_at NBEA neurobeachin 26960 13 13q13 −0.45289 32 208926_at NEU1 sialidase 1 (lysosomal 4758 6 6p21.3 0.27621 sialidase) 33 204107_at NFYA nuclear transcription 4800 6 6p21.3 −0.10057 factor Y, alpha 34 218410_s_at PGP phosphoglycolate 283871 16 16p13.3 −0.13051 phosphatase 35 211159_s_at PPP2R5D protein phosphatase 2, 5528 6 6p21.1 0.218826 regulatory subunit B′, delta isoform 36 205617_at PRRG2 proline rich Gla (G- 5639 19 19q13.33 0.752739 carboxyglutamic acid) 2 37 203038_at PTPRK protein tyrosine 5796 6 6q22.2-q22.3 0.268374 phosphatase, receptor type, K 38 203831_at R3HDM2 R3H domain containing 2 22864 12 12q13.3 −0.04695 39 201779_s_at RNF13 ring finger protein 13 11342 3 3q25.1 0.247392 40 203286_at RNF44 ring finger protein 44 22838 5 5q35.2 −0.07864 41 221524_s_at RRAGD Ras-related GTP binding 58528 6 6q15-q16 0.616503 D 42 212416_at SCAMP1 secretory carrier 9522 5 5q13.3-q14.1 −0.96624 membrane protein 1 43 207707_s_at SEC13 SEC13 homolog (S. 6396 3 3p25-p24 0.706684 cerevisiae) 44 201915_at SEC63 SEC63 homolog (S. 11231 6 6q21 0.383853 cerevisiae) 45 203580_s_at SLC7A6 solute carrier family 7 9057 16 16q22.1 −0.16415 (cationic amino acid transporter, y+ system), member 6 46 212257_s_at SMARCA2 SWI/SNF related, matrix 6595 9 9p22.3 0.152197 associated, actin dependent regulator of chromatin, subfamily a, member 2 47 201794_s_at SMG7 Smg-7 homolog, 9887 1 1q25 −0.33961 nonsense mediated mRNA decay factor (C. elegans) 48 202991_at STARD3 StAR-related lipid 10948 17 17q11-q12 0.579916 transfer (START) domain containing 3 49 210294_at TAPBP TAP binding protein 6892 6 6p21.3 0.04522 (tapasin) 50 217711_at TEK TEK tyrosine kinase, 7010 9 9p21 −0.06112 endothelial 51 212638_s_at WWP1 WW domain containing 11059 8 8q21 −0.37266 E3 ubiquitin protein ligase 1 52 213081_at ZBTB22 zinc finger and BTB 9278 6 6p21.3 −0.16771 domain containing 22 53 216738_at — — — 3 3p25.3 −0.10674 54 220820_at — — — 10 10q11.23 −0.3542 55 222312_s_at — — — 1 1p22.3 −0.11559

Example 5 Performance of Response-Based Predictor in Validation Cohort

FIG. 2 shows the survival outcomes of patients from the independent validation cohort (Table 1A) that were predicted as good responders by the ER-stratified predictor of response (RCB0/I) described in Example 4. Survival is defined by distant relapse-free survival (DRFS) over a period of about 80 months after the initial diagnostic biopsy. These patients have undergone surgery where it was considered appropriate and the ER-positive patients received hormonal therapy (tamoxifen) for 5 years after the surgery. ER-negative patients did not receive any treatment post-surgery.

The plot shows that predicted responders to taxane-containing chemotherapy (FIG. 2) show fewer events resulting in lower distant relapse rate (˜20% relapse rate after 60 months) whereas the remainder show considerably higher relapse rate among the patients (˜40% relapse rate in after 60 months). The overall separation of the two curves, poor responders corresponding to lower survival and good responders corresponding to higher survival, however, are not statistically significant (log-rank test p=0.143). This indicates that the response-based predictor facilitates some separation according to outcomes after therapy but is not strongly predictive enough on its own to distinctly differentiate survival after therapy in this particular validation cohort.

FIG. 3 shows plots of the prediction of the response predictor versus relapse-free survival in ER-positive and ER-negative subsets of the independent validation cohort of Table 1A. The plot shows that predicted responders in ER-positive tumors are not well separated from non-responders over the first 3 years (FIG. 3A), although the predicted non-responders accumulate more events after 3 years, whereas there is a reasonably good separation between responders to taxane-therapy versus non-responders in ER-negative tumors (p=0.094, FIG. 3B). The response-based predictor, therefore, shows a potentially stronger predictive power in ER-negative tumors for outcomes after chemotherapy.

Example 6 Prediction of Chemotherapy Outcome Using a Combination of Relapse-Based and Response-Based Predictors

Based on the performance of the relapse-based or resistance predictor of Example 2 and the response-based predictor of Example 4, combined prediction using the two predictors was studied in the validation cohort (Table 1A). The relapse-based predictor was applied first to the cohort as described in FIG. 1 to obtain low-risk and high-risk patients. The response-based predictor was then applied to the low-risk patients to further stratify them into two groups—called High responders and Intermediate responders. The patients previously identified as high-risk by the relapse-based predictor were labeled here as Low responders.

FIG. 4 shows K-M plots of the cohorts defined by the combined predictor based on relapse (resistance) and response. The plot shows about 29% of patients with an excellent 5-year survival (average 92% DRFS at 60 months) versus the Intermediate and Low responders who show approximately 65% or lower DRFS at 60 months. The separation of the curves is statistically significant (p=0.003). The Intermediate and Low responders may be combined into a single group as non-responders since they had very similar DRFS profiles.

FIG. 5 shows plots of the prediction of the combined predictor versus relapse-free survival in ER-positive (FIG. 5A) and ER-negative (FIG. 5B) subsets of the validation cohort. In both subsets, the High responders as one group are distinctly separated from the Intermediate and Low responders, which together can be considered as Non-responders in both subsets. The responders for the ER-positive tumors have excellent survival (˜100% DRFS at 60 months) versus the non-responders have about 73% DRFS in that time period. The ER-negative tumors, known to have poorer prognosis relative to ER-positive tumors, have an 85% DRFS at 60 months among responders but a much lower DRFS of ˜50% among non-responders. Identifying patients who would be at such high risk despite aggressive chemotherapy would be clinically useful since they can be considered for more advanced therapies or in clinical trials of new therapeutic agents.

Example 7 Chemotherapy Outcomes Prediction Using an Index of Endocrine Sensitivity

The prediction of breast cancer sensitivity to endocrine therapy such as tamoxifen and aromatase inhibitors has been described earlier by measurement of gene expression levels (U.S. Provisional Patent Application, 61/174706). We examined the combination of the sensitivity to endocrine therapy (SET) index with prediction of chemosensitivity using the combined predictor genes described in Example 6.

In this example, the endocrine sensitivity index (as described in U.S. 61/174706) was applied first to the validation cohort of patients shown in Table 1A. The High and Intermediate classes (8.9%) of endocrine sensitivity showed good relapse-free survival (FIG. 6). Therefore, patients who show high and intermediate values of the endocrine sensitivity index will have a good outcome when chemotherapy is combined with endocrine therapy for these patients. The remaining patients (91.1%) need to be evaluated additionally for benefit of chemotherapy using other methods, such as the predictors described in Examples 2 and 4.

The relapse-based predictor (Example 2) and response-based predictor (Example 4), combined as described in Example 6, were applied to the patient samples classified with a low endocrine sensitivity index. Patients identified for chemosensitivity by the predictors of Example 2 and 4 together were then combined with patients with high and intermediate endocrine sensitivity index as responders. FIG. 7 shows the predicted good and poor responders identified by these combined predictors. The poor responders (64.1% of patients) show a larger number of events resulting in lower DRFS (˜60% relapse-free after 60 months) whereas the responder patients (35.9% of total) show considerably higher relapse-free survival among the patients (˜95% relapse-free after 60 months). The two curves, poor responders corresponding to lower survival and good responders corresponding to higher survival, are statistically distinct (p<0.001). This shows that the synergistic use of genomic indices such as the SET index along with the predictor genes in Tables 2 and 3 can very effectively identify patients who will have a good outcome or a poor outcome as a result of chemotherapy.

FIG. 8 shows the performance of the combined predictor separately ER positive and ER negative patients. In ER-positive patients (FIG. 8A), the predicted responders have an excellent outcome as ˜98%% relapse-free survival over 5 years and represent about 35% of the patients whereas the poor responders have a relapse-free survival of 65% in comparison. In ER-negative patients (FIG. 8B), the identified responders have about an 80% relapse-free survival rate in contrast to poor responders who do much worse at 45% relapse-free survival. In both sets of patients, whether ER-positive or ER-negative, the responder and non-responder curves are distinctly separated with statistical significance (p=0.005 for ER-positive and p=0.004 for ER-negative subsets, respectively).

Example 8 Predictor of Poor Response to Chemotherapy

Patients and samples - Patient samples used were those shown in Table 1A. All other laboratory analytic methods were the same as in Example 1.

Methods for building predictors of poor response to chemotherapy—The inventors used the response endpoint RCB-III, representing extensive residual disease after the completion of neoadjuvant chemotherapy, to identify genes that differentiated patients who failed to respond to chemotherapy versus all others in the discovery cohort (Table 1A). Prior to analysis, probes that either had low specificity (those that include extensions _xfri_ in their name) or housekeeping probes (those starting with AFFX) were selected and removed from the candidate probesets. This process removed 2522 probesets. Subsequently, a non-specific filter was applied to retain probesets that has log2-transformed intensity of at least 5 in at least 75% of the arrays. A total of 16289 probesets (73% of all) were retained for further analysis.

The samples in the development cohort were subdivided in ER+ and ER− subsets and in lymph node negative (N0) and lymph positive (NP) subsets within each ER group. Means and standard deviations (SDs) of the 16289 genes were computed for each of the 4 subsets of cases. Within each ER cohort, the means and SDs for N0 and NP subsets were averaged to yield nodal-status adjusted statistics. These means and SDs were then used to scale the expression values of all probesets using the corresponding statistics for ER+ or ER− cases.

Each probeset was evaluated for differential expression in the two responder groups (RCB-III vs rest) using an unequal variance t-statistic based on the trimmed means and trimmed standard deviations in the two groups using a trim fraction of 0.025 (i.e. the lowest 2.5% and highest 2.5% values were eliminated and the statistics were calculated on the remaining 95% of the observations in each group). Degrees of freedom for the unequal variance t-statistic were estimated based on Satterthwaite's approximation (Armitage, Berry & Matthews, 2002). The significance of association of each probe set with response was assessed based on the unequal variance t-statistic. P-values for the significance of each probeset were calculated from the t-distribution with the corresponding degrees of freedom.

To account for sampling variability in the training dataset, the differential expression analysis for each probeset described in the previous paragraph was performed repeatedly using a bootstrap procedure in which cases were sampled with replacement to generate bootstrapped datasets of the same size as the original dataset. This process was repeated 499 times, thus generating 500 estimates for the p-values of each probeset. The association of each probeset with distant relapse risk was assessed within each bootstrapped dataset at a critical significance level of 0.00075 to account for multiple testing. Those probesets that were called significant in at least 30% of the bootstrap replicates were selected as candidate probesets. This process was applied separately to the ER-positive and ER-negative cases in the training dataset and resulted in 256 and 202 candidate probesets in the ER+ and ER− subsets.

In developing the RCB-based chemotherapy response predictor, the inventors used an approach that combines feature selection and model discovery using a multivariate penalized approach called Gradient Directed Regularization developed by Prof. J. Friedman at Stanford University, a description of which can be found on the World Wide Web at stat.stanford.edu/˜jhf/ftp/pathlite.pdf. The informative genes are selected through penalization using the maximization of the area under the ROC curve (AUC) as the optimization criterion. Ma and Huang have previously used a similar approach for disease classification (Ma, 2006).

For predictor discovery and evaluation the inventors followed a cross-validation protocol. First, the input dataset is randomly partitioned into a training set and a test set. A 5-fold cross-validation for a 4:1 split stratified by response group between training and test sets was used (Dudoit, 2002). The training set consisting of ⅘ of the original data is used to develop the predictor. The algorithm starts with the same initial list of candidate genes that were determined through the bootstrap procedure and iteratively refines the predictor by selecting genes that contribute in maximizing the AUC of the candidate predictor. The maximum level of penalization is used to derive the most parsimonious predictors. Since different optimal reporter gene sets might result from the different internal cross-validation folds, the number of times each gene is selected is tracked to provide a measure of its importance or its reliability. The trained predictor is then tested on the ⅕ hold-out part of the training dataset and its performance is evaluated based on the AUC.

The entire process of randomly splitting the data to a training- and a test-set was repeated 499 times to obtain the distributions and summary statistics of the performance metrics from the cross-validated replicates.

The final predictors for ER+ and ER− subsets used 73 probesets and 54 probesets respectively to make the predictions. The probesets, genes that they encode for, and their weights (coefficients) are shown in Table 4. The risk score is calculated by multiplying the scaled log2-transformed expression level of each gene in a given sample by its corresponding weight and then adding up the weighted expression values for all genes in the signature. The following formula describes the score calculation for sample i:

$y_{i} = \left\{ \begin{matrix} {{\sum\limits_{j = 1}^{K +}{w_{j}^{+}z_{ij}^{+}}},} & {{if}\mspace{14mu} {ER}\mspace{14mu} {positive}} \\ {{\sum\limits_{j = 1}^{K -}{w_{j}^{-}z_{ij}^{-}}},} & {{if}\mspace{14mu} {ER}\mspace{14mu} {negative}} \end{matrix} \right.$

-   where w_(j) is the weight of gene j in the signature, z_(ij) is the     log2-transformed and scaled expression value of gene j in sample i,     K is the number of genes in the signature, and the + or − symbols     refer to the ER+ and ER− signatures.

A cut point was selected to dichotomize the risk score and predict two risk classes. The optimal cutoff was selected in order to maximize the accuracy of the prediction. A cutoff of 0 was selected for both the ER+ and ER− scores. Positive scores signify “resistant” or poor-responder and a zero or negative score signifies “non-resistant”.

TABLE 4 Genes used for prediction of poor response, RCB-III, in ER-stratified patient subsets Probe Set Symbol Description GeneID Chromosome Cytoband Weight ER-Positive 1 200045_at ABCF1 ATP-binding cassette, 23 6 6p21.33 −0.1287 sub-family F (GCN20), member 1 2 218868_at ACTR3B ARP3 actin-related 57180 7 7q36.1 −0.073 protein 3 homolog B (yeast) 3 213532_at ADAM17 ADAM 6868 2 2p25 −0.3194 metallopeptidase domain 17 4 217090_at ADAM3A ADAM 1587 8 8p11.23 0.3763 metallopeptidase domain 3A (cyritestin 1) 5 205013_s_at ADORA2A adenosine A2a 135 22 22q11.23 0.1786 receptor 6 208042_at AGGF1 angiogenic factor with 55109 5 5q13.3 0.1425 G patch and FHA domains 1 7 215789_s_at AJAP1 adherens junctions 55966 1 1p36.32 −0.111 associated protein 1 8 221825_at ANGEL2 angel homolog 2 90806 1 1q32.3 0.5463 (Drosophila) 9 202631_s_at APPBP2 amyloid beta 10513 17 17q21-q23 −0.1027 precursor protein (cytoplasmic tail) binding protein 2 10 200011_s_at ARF3 ADP-ribosylation 377 12 12q13 0.3083 factor 3 11 202492_at ATG9A ATG9 autophagy 79065 2 2q35 −0.6807 related 9 homolog A (S. cerevisiae) 12 212930_at ATP2B1 ATPase, Ca++ 490 12 12q21.3 0.0737 transporting, plasma membrane 1 13 218789_s_at C11orf71 chromosome 11 open 54494 11 11q14.2-q14.3 0.2824 reading frame 71 14 219022_at C12orf43 chromosome 12 open 64897 12 12q 0.3528 reading frame 43 15 214322_at CAMK2G calcium/calmodulin- 818 10 10q22 −0.0176 dependent protein kinase II gamma 16 218384_at CARHSP1 calcium regulated 23589 16 16p13.2 0.5253 heat stable protein 1, 24 kDa 17 212586_at CAST calpastatin 831 5 5q15 −0.0498 18 218592_s_at CECR5 cat eye syndrome 27440 22 −0.4437 chromosome region, candidate 5 19 218439_s_at COMMD10 COMM domain 51397 5 5q23.1 0.1117 containing 10 20 211808_s_at CREBBP CREB binding protein 1387 16 16p13.3 0.1494 21 209164_s_at CYB561 cytochrome b-561 1534 17 17q11-qter −0.3429 22 203979_at CYP27A1 cytochrome P450, 1593 2 2q33-qter −0.3785 family 27, subfamily A, polypeptide 1 23 216874_at DKFZp686O1327 hypothetical gene 401014 2 2q22.3 1 supported by BC043549; BX648102 24 204797_s_at EML1 echinoderm 2009 14 14q32 0.2037 microtubule associated protein like 1 25 218692_at GOLSYN Golgi-localized protein 55638 8 8q23.2 0.174 26 202453_s_at GTF2H1 general transcription 2965 11 11p15.1-p14 −0.3144 factor IIH, polypeptide 1, 62 kDa 27 221046_s_at GTPBP8 GTP-binding protein 8 29083 3 3q13.2 −0.118 (putative) 28 208886_at H1F0 H1 histone family, 3005 22 22q13.1 0.028 member 0 29 205426_s_at HIP1 huntingtin interacting 3092 7 7q11.23 0.4815 protein 1 30 202983_at HLTF helicase-like 6596 3 3q25.1-q26.1 −0.1866 transcription factor 31 217145_at IGKC immunoglobulin kappa 3514 2 2p12 −0.035 constant 32 204863_s_at IL6ST interleukin 6 signal 3572 5 5q11 −0.6475 transducer (gp130, oncostatin M receptor) 33 211817_s_at KCNJ5 potassium inwardly- 3762 11 11q24 0.3023 rectifying channel, subfamily J, member 5 34 201776_s_at KIAA0494 KIAA0494 9813 1 1pter-p22.1 −0.3831 35 209212_s_at KLF5 Kruppel-like factor 5 688 13 13q22.1 −0.1623 (intestinal) 36 212271_at MAPK1 mitogen-activated 5594 22 22q11.2 0.1979 protein kinase 1 37 206904_at MATN1 matrilin 1, cartilage 4146 1 1p35 −0.4397 matrix protein 38 206961_s_at MED20 mediator complex 9477 6 6p21.1 0.1547 subunit 20 39 213403_at MFSD9 major facilitator 84804 2 2q12.1 0.3304 superfamily domain containing 9 40 209733_at MID2 midline 2 11043 X Xq22.3 0.1227 41 218205_s_at MKNK2 MAP kinase 2872 19 19p13.3 0.1801 interacting serine/threonine kinase 2 42 209973_at NFKBIL1 nuclear factor of 4795 6 6p21.3 −0.0068 kappa light polypeptide gene enhancer in B-cells inhibitor-like 1 43 217963_s_at NGFRAP1 nerve growth factor 27018 X Xq22.2 0.201 receptor (TNFRSF16) associated protein 1 44 207400_at NPY5R neuropeptide Y 4889 4 4q31-q32 0.0984 receptor Y5 45 202097_at NUP153 nucleoporin 153 kDa 9972 6 6p22.3 −0.1197 46 220631_at OSGEPL1 O-sialoglycoprotein 64172 2 2q32.2 0.2148 endopeptidase-like 1 47 205077_s_at PIGF phosphatidylinositol 5281 2 2p21-p16 0.5495 glycan anchor biosynthesis, class F 48 220811_at PRG3 proteoglycan 3 10394 11 11q12 0.2689 49 208733_at RAB2A RAB2A, member RAS 5862 8 8q12.1 0.581 oncogene family 50 206066_s_at RAD51C RAD51 homolog C (S. 5889 17 17q22-q23 −0.0517 cerevisiae) 51 206290_s_at RGS7 regulator of G-protein 6000 1 1q23.1 0.0092 signaling 7 52 214519_s_at RLN2 relaxin 2 6019 9 9p24.1 0.103 53 206805_at SEMA3A sema domain, 10371 7 7p12.1 0.1132 immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A 54 208941_s_at SEPHS1 selenophosphate 22929 10 10p14 −0.6301 synthetase 1 55 213755_s_at SKI v-ski sarcoma viral 6497 1 1q22-q24 −0.1078 oncogene homolog (avian) 56 202667_s_at SLC39A7 solute carrier family 7922 6 6p21.3 −0.1376 39 (zinc transporter), member 7 57 216611_s_at SLC6A2 solute carrier family 6 6530 16 16q12.2 −0.0064 (neurotransmitter transporter, noradrenalin), member 2 58 211805_s_at SLC8A1 solute carrier family 8 6546 2 2p23-p22 −0.248 (sodium/calcium exchanger), member 1 59 205596_s_at SMURF2 SMAD specific E3 64750 17 17q22-q23 −0.1446 ubiquitin protein ligase 2 60 203054_s_at TCTA T-cell leukemia 6988 3 3p21 0.2818 translocation altered gene 61 218099_at TEX2 testis expressed 2 55852 17 17q23.3 −0.0149 62 217121_at TNKS tankyrase, TRF1- 8658 8 8p23.1 −0.5943 interacting ankyrin- related ADP-ribose polymerase 63 220415_at TNNI3K TNNI3 interacting 51086 1 1p31.1 0.3122 kinase 64 209593_s_at TOR1B torsin family 1, 27348 9 9q34 −0.0834 member B (torsin B) 65 215796_at TRD@ T cell receptor delta 6964 14 14q11.2 0.4491 locus 66 210541_s_at TRIM27 tripartite motif- 5987 6 6p22 −0.0174 containing 27 67 213563_s_at TUBGCP2 tubulin, gamma 10844 10 10q26.3 −0.169 complex associated protein 2 68 221839_s_at UBAP2 ubiquitin associated 55833 9 9p13.3 −0.0133 protein 2 69 213822_s_at UBE3B ubiquitin protein ligase 89910 12 12q24.11 −0.4683 E3B 70 221746_at UBL4A ubiquitin-like 4A 8266 X Xq28 −0.0227 71 219740_at VASH2 vasohibin 2 79805 1 1q32.3 −0.1995 72 205877_s_at ZC3H7B zinc finger CCCH-type 23264 22 22q13.2 −0.9818 containing 7B 73 218413_s_at ZNF639 zinc finger protein 639 51193 3 3q26.33 −0.1572 ER-Negative 1 214919_s_at ANKHD1- ANKHD1- 404734 5 5q31.3 0.1134 EIF4EBP3 EIF4EBP3 readthrough 2 202955_s_at ARFGEF1 ADP-ribosylation 10565 8 8q13 0.0616 factor guanine nucleotide- exchange factor 1(brefeldin A- inhibited) 3 203576_at BCAT2 branched chain 587 19 19q13 −0.1544 aminotransferase 2, mitochondrial 4 202047_s_at CBX6 chromobox 23466 22 22q13.1 0.0673 homolog 6 5 220674_at CD22 CD22 molecule 933 19 19q13.1 0.1582 6 208022_s_at CDC14B CDC14 cell 8555 9 9q22.32-q22.33 −0.4312 division cycle 14 homolog B (S. cerevisiae) 7 204250_s_at CEP164 centrosomal 22897 11 11q23.3 0.1607 protein 164 kDa 8 218597_s_at CISD1 CDGSH iron sulfur 55847 10 10q21.1 0.6177 domain 1 9 206073_at COLQ collagen-like tail 8292 3 3p25 −0.033 subunit (single strand of homotrimer) of asymmetric acetylcholinesterase 10 208303_s_at CRLF2 cytokine receptor- 64109 X, Y Xp22.3 −0.0413 like factor 2 11 217047_s_at FAM13A family with 10144 4 4q22.1 −0.1603 sequence similarity 13, member A 12 212484_at FAM89B family with 23625 11 11q23 −0.0232 sequence similarity 89, member B 13 204437_s_at FOLR1 folate receptor 1 2348 11 11q13.3-q14.1 −1 (adult) 14 203314_at GTPBP6 GTP binding 8225 X, Y Xp22.33 0.0926 protein 6 (putative) 15 210964_s_at GYG2 glycogenin 2 8908 X Xp22.3 −0.364 16 212431_at HMGXB3 HMG box domain 22993 5 5q32 0.0875 containing 3 17 211616_s_at HTR2A 5- 3356 13 13q14-q21 0.1049 hydroxytryptamine (serotonin) receptor 2A 18 204990_s_at ITGB4 integrin, beta 4 3691 17 17q25 −0.2769 19 207012_at MMP16 matrix 4325 8 8q21.3 0.1034 metallopeptidase 16 (membrane- inserted) 20 212251_at MTDH Metadherin 92140 8 8q22.1 0.7935 21 202039_at MYO18A myosin XVIIIA 399687 17 17q11.2 0.1596 22 222018_at NACA nascent 4666 12 12q23-q24.1 0.1843 polypeptide- associated complex alpha subunit 23 209519_at NCBP1 nuclear cap 4686 9 9q34.1 −0.4186 binding protein subunit 1, 80 kDa 24 213032_at NFIB nuclear factor I/B 4781 9 9p24.1 0.1829 25 215818_at NUDT7 nudix (nucleoside 283927 16 16q23.1 −0.1766 diphosphate linked moiety X)-type motif 7 26 218271_s_at PARL presenilin 55486 3 3q27.1 −0.0708 associated, rhomboid-like 27 204049_s_at PHACTR2 phosphatase and 9749 6 6q24.2 0.1352 actin regulator 2 28 217806_s_at POLDIP2 polymerase (DNA- 26073 17 17q11.2 0.3128 directed), delta interacting protein 2 29 206653_at POLR3G polymerase (RNA) 10622 5 5q14.3 −0.3632 III (DNA directed) polypeptide G (32 kD) 30 210831_s_at PTGER3 prostaglandin E 5733 1 1p31.2 −0.0066 receptor 3 (subtype EP3) 31 213933_at PTGER3 prostaglandin E 5733 1 1p31.2 0.0187 receptor 3 (subtype EPS) 32 208393_s_at RAD50 RAD50 homolog 10111 5 5q31 −0.1057 (S. cerevisiae) 33 221705_s_at SIKE1 suppressor of 80143 1 1p13.2 −0.2882 IKBKE 1 34 211112_at SLC12A4 solute carrier 6560 16 16q22.1 −0.1596 family 12 (potassium/chloride transporters), member 4 35 215294_s_at SMARCA1 SWI/SNF related, 6594 X Xq25 0.056 matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 36 215458_s_at SMURF1 SMAD specific E3 57154 7 7q22.1 −0.1767 ubiquitin protein ligase 1 37 215860_at SYT12 synaptotagmin XII 91683 11 11q13.2 −0.023 38 222173_s_at TBC1D2 TBC1 domain 55357 9 9q22.33 −0.124 family, member 2 39 204147_s_at TFDP1 transcription factor 7027 13 13q34 0.1725 Dp-1 40 206260_at TGM4 transglutaminase 7047 3 3p22-p21.33 0.2701 4 (prostate) 41 212963_at TM2D1 TM2 domain 83941 1 1p31.3 0.1779 containing 1 42 213882_at TM2D1 TM2 domain 83941 1 1p31.3 0.1487 containing 1 43 219182_at TMEM231 transmembrane 79583 16 16q23.1 −0.2436 protein 231 44 209344_at TPM4 tropomyosin 4 7171 19 19p13.1 0.3404 45 217056_at TRD@ T cell receptor 6964 14 14q11.2 0.0697 delta locus 46 217065_at TRD@ T cell receptor 6964 14 14q11.2 0.0128 delta locus 47 203701_s_at TRMT1 TRM1 tRNA 55621 19 19p13.2 0.187 methyltransferase 1 homolog (S. cerevisiae) 48 201797_s_at VARS valyl-tRNA 7407 6 6p21.3 −0.5888 synthetase 49 208453_s_at XPNPEP1 X-prolyl 7511 10 10q25.3 0.5107 aminopeptidase (aminopeptidase P) 1, soluble 50 213081_at ZBTB22 zinc finger and 9278 6 6p21.3 0.3968 BTB domain containing 22 51 206448_at ZNF365 zinc finger protein 22891 10 10q21.2 0.3809 365 52 212867_at — — — 8 8q13.3 0.4115 53 213879_at — — — 17 17q25.1 −0.4574 54 222174_at — — — 14 — 0.017

Example 9 Prediction of Chemotherapy Outcomes Combining Poor Response as Endpoint

Survival outcomes of patients predicted as responders and non-responders were assessed by using the predictor of RCB-III described in Example 8 used as a combined algorithm with predictors of Examples 2 and 4 and the sensitivity to endocrine therapy (SET) index of Example 7. Survival is defined by distant relapse-free survival (DRFS) over a period of about 80 months. These patients have undergone surgery where it was considered appropriate and the ER-positive patients received hormonal therapy (tamoxifen) for 5 years after the surgery. ER-negative patients did not receive any treatment post-surgery. We combined the individual predictions into a testing algorithm (FIG. 9) for predicted sensitivity to adjuvant treatment of HER2-negative breast cancer with taxane-anthracycline chemotherapy: 1) sensitivity to endocrine therapy (SET) assessed based on the published 165-gene index of the most ER-correlated genes (high or intermediate SET index) that independently predicts survival following adjuvant endocrine or chemoendocrine therapy¹³; 2) resistance to chemotherapy predicted either by early distant relapse events or by extensive residual disease after neoadjuvant chemotherapy; and 3) sensitivity (pathologic response) to chemotherapy.

The predictive test (algorithm) was applied to the discovery cohort of 310 samples (FIG. 10A) and then evaluated in the independent validation cohort of 198 patients (99% clinical Stage II-III) who received sequential taxane-anthracycline chemotherapy then endocrine therapy (if ER+). The validation cohort had a pathologic response rate of pCR 25% and of pCR or RCB-I 30%, median follow up of 3 years, and an average 3-year baseline DRFS of 79% (95% CI 74 to 85). The 3-year DRFS (NPV) was 92% (95% CI 85 to 100), and there was significant absolute risk reduction (ARR) of 18% (95% CI 6 to 28), in 28% of patients who were predicted to be treatment-sensitive. The 3-year point estimate of DRFS for those predicted to be treatment-insensitive was 75% (95% CI 67 to 82). Overall, we observed a significant association between predicted sensitivity to treatment and DRFS (p=0.002; FIG. 10B). In 91 tumors with low SET and evaluated for RCB, excellent response from chemotherapy (pCR or RCB-I) was observed in 56% (95% CI 31 to 78) of those predicted to be treatment-sensitive.

Of note, 3-year DRFS in patients predicted to be treatment-sensitive at the time of diagnosis was similar to the 3-year DRFS of 93% (95% CI 85 to 100) in the 21% of patients in the validation cohort who achieved pathologic complete response (pCR) after completion of neoadjuvant chemotherapy. Also, 3-year DRFS for predicted treatment-insensitive was identical to the 3-year DRFS of 75% (95% CI 68 to 83) in those who had residual disease (RD) (FIG. 10C). Furthermore, DRFS estimates for the predicted treatment-sensitive and the actual pCR groups were unchanged at 5 years, and were identical at 65% (95% CI 56 to 75) for the predicted treatment-insensitive and for the actual RD groups:

Treatment Sensitivity According to ER Status: There were 30% and 26% of patients with predicted sensitivity to treatment in the ER+/HER2- and ER−/HER2-subsets, respectively, and both had significantly favorable prognosis (FIG. 11A-B). The treatment sensitive patients identified by test in the ER+/HER2-subset had excellent DRFS (NPV) of 97% (95% CI 91 to 100) and a significant ARR of 11% (95% CI 0.1 to 21) at 3 years of follow up. In the low SET subset of ER+/HER2-, PPV for pathologic response was 42% (95% CI 15 to 72) in 20% who were predicted treatment-sensitive. For ER−/HER2-patients, the PPV for 3-year relapse was 43% (95% CI 28 to 55) if predicted treatment-insensitive. Patients predicted to be treatment-sensitive had considerably improved 3-year DRFS (NPV 83% (95% CI 68 to 100)) and significant ARR of 26% (95% CI 4 to 48) overall, and PPV for pathologic response of 83% (95% CI 36-100).

Performance of the Predictive Test in Other Relevant Subsets The association between predicted treatment sensitivity and DRFS appears to be unrelated to the type of taxane therapy administered (FIG. 11C-D). The 3-year DRFS was 90% (95% CI 80 to 100) in the subset who received 12 cycles of weekly paclitaxel, and 96% (95% CI 88 to 100) for 4 cycles of 3-weekly docetaxel with capecitabine. Also, the 3-year DRFS was 93% (95% CI 84 to 100) in 128 clinically node-positive patients, with significantly improved DRFS compared to those predicted to be insensitive (p=0.003). The 3-year DRFS was 91% (95% CI 81 to 100) in 70 clinically node-negative patients, but was not significantly different from predicted insensitivity.

Comparison of the Predictive Test with Clinical-Pathologic Parameters Genomic predictions were independently and significantly associated with risk of distant relapse or death (sensitive versus insensitive; HR 0.19; 95% CI 0.07 to 0.55; p=0.002), after adjusting for standard clinical-pathologic parameters (Table 5). Addition of the genomic prediction to a multivariate Cox model of the clinical-pathologic factors significantly increased the model's predictive utility (likelihood ratio of complete model versus clinical model 13.8, p<0.001). In this model, higher clinical tumor stage (tumor stage T3 or T4 versus T1 or T2; HR 2.13;

95% CI 1.13 to 4.02; p=0.02) and ER-negative status (ER status positive versus negative; HR 0.34; 95% CI 0.18 to 0.65; p=0.001) were associated with statistically significant greater risk of distant relapse or death.

TABLE 5 MULTIVARIATE Cox Regression Analysis of Association with DRFS Validation Cohort (N = 183)* P Factor Hazard Ratio (95% CI) value Age (>50 vs ≦50) 0.53 (0.27 to 1.04) 0.063 Clinical Nodal Status (pos vs neg) 1.76 (0.84 to 3.67) 0.134 Clinical Tumor Stage (T3 or T4 vs T1 2.13 (1.13 to 4.02) 0.020 or T2) Histologic Grade (3 vs 1 or 2) 0.64 (0.32 to 1.29) 0.208 ER Status (THC positive vs negative) 0.34 (0.18 to 0.65) 0.001 Taxane (docetaxel vs paclitaxel) 0.92 (0.49 to 1.73) 0.795 Prediction (Rx Sensitive vs Insensitive) 0.19 (0.07 to 0.56) 0.002 *Fifteen cases were excluded from the multivariate analysis due to incomplete data. Likelihood ratio test for the addition of Genomic Prediction to the model was 13.8 on one degree of freedom, p = 0.0002. The Hazard Ratio is a measure of the risk of distant relapse or death; vs, versus; ER, estrogen receptor.

Example 10 Comparison with Other Predictive Genomic Signatures

The entire predictive test algorithm described in FIG. 9 had PPV of 56% (95% CI 31 to 78) for pathologic response prediction in the validation cohort (Table 6) after excluding patients with predicted endocrine sensitivity (high or intermediate SET). We also evaluated other phenotypic predictors that have published association with higher probability of pCR to neoadjuvant chemotherapy, have a pre-defined threshold for prediction of pCR that was based on Affymetrix microarray data, and that we have confirmed to be correctly calculated in our hands: the 96-gene genomic grade index (GGI) to define high versus low grade (high GGI predicted pCR) (Liedtke et al., 2009), a 52-gene signature (PAM50) to assign intrinsic subtype (basal-like, HER2 and luminal B subtypes predicted pCR) (Parker et al., 2009), and a 30-gene signature (DLDA30) developed to predict pCR versus residual disease (Hess, Anderson et al., 2006). These tests were significantly predictive of pathologic response in the discovery cohort (lower 95% confidence limit of the PPV greater than the baseline pCR rate of 19% and pCR or RCB-I rate of 29%), and the tests had NPV of 84% or greater (Table 6). Performance in the validation cohort was similar, but not all tests had PPV and NPV that was significantly greater than the baseline response rates (pCR rate of 25% and pCR or RCB-I rate of 30%). The entire prediction algorithm (FIGS. 9), demonstrated significantly better DRFS for patients who were predicted to be treatment-sensitive (Table 6). The other tests (GGI, PAM50, DLDA30) demonstrated worse DRFS for patients who were predicted to have chemosensitive breast cancer (FIG. 12), as indicated by their negative ARR (Table 6).

The performance of the different genomic signatures for predicting 3-year DRFS was compared on the basis of the diagnostic likelihood ratio (DLR), which is clinically useful statistic for summarizing the diagnostic accuracy of tests (Deeks and Altman, 2004). The DLR+ summarizes how many times a positive test (predicted distant relapse or treatment insensitive) is more likely among patients who experience distant metastasis within 3 years, compared to those who do not. The DLR− is a similar metric for a negative test (predicted absence of relapse or treatment sensitive), which is more relevant in the context of this test. A clinically useful test associated with the presence of relapse should have DLR+>1, whereas a test associated with the absence of relapse should have DLR−<1. Another useful property of the DLR is that it allows calculation of the post-test odds of relapse, simply by multiplying the pre-test odds of relapse by the DLR. The odds ratio (OD), defined as DLR+/DLR−, is also related to the coefficient of a logistic regression model of the binary genomic test for predicting the binary relapse outcome. The values summarized in Table 7 were calculated from the K-M estimates of DRFS for the two predicted groups from each genomic predictor, for the overall validation cohort and for the ER-positive and ER-negative subsets.

The predictive test of Example 9 (last entry in Table 7) is the only test with a significant DLR− (0.33, 0.27, 0.35 in the overall validation cohort and ER+, ER− subsets), indicating a 3-fold reduction in the odds of distant relapse in the presence of a negative test result (predicted treatment sensitive). The DLR+ of the genomic predictor was >1 in all 3 cohorts, but was not significant. The ER-stratified predictor of pCR/RCB-I showed consistent but not significant metrics. The first three genomic predictors showed paradoxical statistics (DLR+<1 and DLR−>1), i.e. a positive test result (predicted relapse) was associated with lower odds of relapse and vice versa.

TABLE 6 Performance of Genomic Signatures for Predicting Pathologic Response and 3-year DRFS Prediction of Pathologic Response Prediction of Distant Relapse or Death Within 3 Years Discovery Cohort Validation Cohort Discovery Cohort (N = 310) Validation Cohort (N = 198) N N % % NPV % NPV Predictor (% Resp) % PPV % NPV (% Resp) % PPV NPV (DRFS) % PPV % ARR (DRFS) % PPV % ARR Genomic 301 36 88 101  40 84 72 14 −14 72  7 −21 Grade  (29) (30 to (79 to (30) (28 to (70 to (65 to (6 to (−25 to (64 to (1 to (−30 to Index 43) 93) 54) 93) 79) 22) −3) 80) 13) −10) (High) Genomic 301 40 85 101  40 78 66 13 −20 72 12 −16 Subtype  (29) (32 to (78 to (30) (25 to (65 to (58 to (7 to (−31 to (62 to (6 to (−27 to Classifier 48) 90) 56) 87) 76) 19) −10) 81) 20) −5) (Luminal B or Basal- like) Genomic 301 46 83 101  40 75 62 15 −24 62 10 −28 Predictor  (29) (37 to (77 to (30) (24 to (63 to (52 to (9 to (−36 to (50 to (4 to (−41 to of pCR 55) 88) 58) 85) 73) 20) −12) 73) 16) −16) ER- 301 69 100  101  42 81 85 30   15 82 24    5 stratified  (29) (60 to (98 to (30) (28 to (68 to (78 to (22 to (4 to (74 to (14 to (−7 to Genomic 77) 100) 57) 91) 93) 37) 25) 90) 32) 16) Predictor of pCR/RCB-I ^(§) Predictive 256 78 84 91 56 73 95 36   31 92 25   18 Test (Rx  (31) (66 to 78 to (33) (31 to (61 to (91 to (27 to (22 to (85 to (18 to (6 to Sensitive) ^(§) ^(¶) ^(#) 88) 89) 78) 82) 100) 44) 41) 100) 33) 28) N, number or patients evaluated; %, percent; Resp, pathologic response rate; PPV, positive predictive value; NPV, negative predictive value; DRFS, distant relapse-free survival estimate at 3 years; ARR, absolute risk reduction for event within 3 years if predicted to be treatment-sensitive (−, any negative risk reduction was in favor of predicted treatment-insensitive). The 95% confidence intervals (parentheses) for PPV and NPV for prediction of pathologic response were based on binomial approximation. ^(§) Performance of the pCR predictor on the discovery cohort is optimistically biased because the predictor was trained on a subset of these samples. Performance of the pCR/RCB-I predictor and of the overall genomic prediction test on the discovery cohort represents resubstitution performance, since the predictors were trained on the same cohort. ^(¶) Genomic prediction of pathologic response was evaluated in the SET-Low subset in both cohorts. ^(#) Performance of the predictive test is optimistically biased in the discovery cohort because a component of the test was trained on DRFS events to define resistance.

TABLE 7 Comparison of Genomic Signatures Performance for Predicting 3-year DRFS Validation Cohort (N = 198) ER-positive Subset (N = 123) ER-negative Subset (N = 74) DLR+ DLR− OR DLR+ DLR− OR DLR+ DLR− OR Predictor (95% CI) (95% CI) (95% CI) (95% CI) (95% CI) (95% CI) (95% CI) (95% CI) (95% CI) Genomic .30 1.50 .2  .62 1.41 .44 .17 1.20 .14 Grade (.06 to (.97 to (.04 to (.13 to (.45 to (.06 to (.0 to (.73 to (.0 to Index 0.63) 2.20) .47) 1.33) 2.88) 1.71) .77) 2.01) .70) (High) Genomic .55 1.53 .36 .81 1.32 .62 .60 1.21 .50 Subtype (.24 to (.97 to (.14 to (.23 to (.36 to (.15 to (.15 to (.69 to (.12 to Classifier .96) 2.33) .74) 1.60) 2.64) 2.80) 1.56) 2.14) 1.50) (Luminal B or Basal- like) Genomic .43 2.39 .18 .86 1.98 .43 .28 1.31 .21 Predictor (.18 to (1.41 to (.07 to (.33 to (.01 to (.10 to (.0 to (.77 to (.0 to of pCR .73) 3.96) .37) 1.50) 6.37) 88.1) .92) 2.25) .77) ER- 1.18   .85 1.39  1.07   .93 1.15  1.70   .68 2.50  stratified (.65 to (.46 to (.66 to (.35 to (.16 to (.31 to (.79 to (.32 to (.88 to Genomic 1.83) 1.36) 2.93) 2.11) 2.03) 6.61) 3.65) 1.27) 7.03) Predictor of pCR/RCB-I Predictive 1.32   .33 4.01  1.33   .27 4.88  1.33   .35 3.78  Test (Rx (.84 to (.07 to (1.55 to (.56 to (.01 to (1.05 to (.76 to (.01 to (1.16 to Sensitive) 1.93) .78) 21.6) 2.34) 0.98) 206) 2.30) .99) 138) DLR: Diagnostic likelihood ratio; DLR+: DLR given a positive test result (predicted treatment insensitive); DLR−: DLR given a negative test result (predicted treatment sensitive); OR: odd ratio of a positive test result over a negative test result (DLR+/DLR−); CI: confidence interval. Confidence intervals were calculated through bootstrap with 999 iterations

Example 11 Analysis of Patient Samples Using Predictor for Assessing Outcome of Therapy

FIG. 13 shows a schematic of how a patient sample may be collected at the time of biopsy or at the time of surgery, and analyzed in a laboratory to produce a result from the predictor to be used to assess likely outcome of chemotherapy. A tumor sample, collected as a needle biopsy or a fresh tumor sample from the excised tumor after surgery is added to a pre-supplied tube containing RNA preservative solution. The tube is shipped overnight to a qualified laboratory for analysis of gene expression.

RNA is extracted in a manner described in Example 1. A gene chip such as Affymetrix U133A (Affymetrix, Inc., Santa Clara, CA) is used to analyze the expression levels of genes of Tables 2, 3 and 4. The resulting expression values are then normalized as described in Examples 2, 4, and 8, and weighted according to their respective coefficients to calculate the predictor score. Using cut-off values for the predictor score, a patient's tumor can be classified as either a High Score (good outcome from therapy) or a Low Score (poor outcome of therapy). The analyses could be completed within 5-7 days from receipt of a tumor sample to provide a report on results to the requesting physician. Decisions may be made by physicians regarding the inclusion of a certain therapy if the likely outcome is good or alternatively, to consider additional aggressive therapy regimens for the patient in the likely event of a poor outcome.

REFERENCES

The following references, to the extent that they provide exemplary procedural or other details supplementary to those set forth herein, are specifically incorporated herein by reference.

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What is claimed is:
 1. A method of evaluating a cancer patient comprising the steps of: (a) evaluating gene expression levels in a patient sample comprising cancer cells or an RNA sample isolated from such a patient sample, wherein a plurality of genes to be evaluated are selected from one or more of Table 2, Table 3, and Table 4; (b) calculating a predictor score using the gene expression levels; and (c) assessing the likelihood of a therapeutic outcome using the predictor score.
 2. The method of claim 1, further comprising identifying a cancer patient with a disease state classified as a residual disease state prior to evaluation.
 3. The method of claim 1, wherein the therapeutic outcome distant relapse-free survival (DRFS).
 4. The method of claim 1, wherein the transcriptional profile index comprises 5 or more genes of Table 2, Table 3, and Table
 4. 5. The method of claim 1, wherein the transcriptional profile index comprises 10 or more genes of Table 2, Table 3, and Table
 4. 6. The method of claim 1, wherein the transcriptional profile index comprises 20 or more genes of Table 2, Table 3, and Table
 4. 7. The method of claim I, wherein the transcriptional profile index comprises 30 genes of Table 2, Table 3, and Table
 4. 8. The method of claim 1, wherein the transcriptional profile index comprises 60 genes of Table 2, Table 3, and Table
 4. 9. The method of claim 1, wherein the transcriptional profile index comprises all genes of Table 2, Table 3, and Table
 4. 10. The method of claim 1, further comprising determining Her2-neu and/or estrogen receptor status of the patient sample.
 11. The method of claim 1, wherein the predictor score includes evaluation of tumor size, cellularity of tumor bed, and/or nodal burden.
 12. The method of claim 1, further comprising providing a treatment recommendation depending on the predictor classification.
 13. The method of claim 12, wherein the treatment is a combination of one or more cancer therapy.
 14. The method of claim 13, wherein the treatment is hormonal therapy and/or chemotherapy.
 15. The method of claim 14, wherein the chemotherapy consists of taxane and anthracycline therapy.
 16. The method of claim 1, wherein preparing the predictor score comprises the steps of: (a) obtaining data associated with a plurality of breast cancer patients comprising measuring expression levels of a plurality of genes in samples from the patients; (b) partitioning the data into a first and second dataset; (c) evaluating the data and identifying data associated with a particular treatment outcome; (d) selecting a set of genes whose expression levels are indicative of therapeutic outcome
 17. The method of claim 16, wherein the index includes evaluation of survival of the patient population sampled for all or part of the reference population of tumor samples.
 18. The method of claim 17, wherein the method includes evaluation of distant relapse-free survival (DRFS) of the patient population.
 19. A kit to determine responsiveness of a cancer comprising: (a) reagents for determining expression levels of a plurality of genes selected from Table 2, Table 3, and Table 4 or combinations thereof; and (b) software encoding an algorithm for calculating a predictor score based on the analysis of the gene expression levels.
 20. A system for providing assessment of a sample relative to a gene expression index, the system comprising: (a) an application server comprising an input manager to receive expression data from a user for a plurality of genes selected from Table 2, Table 3, and Table 4 or combinations thereof obtained from a patient sample or an RNA sample from such patient sample; and (b) a network server comprising an output manager constructed and arranged to provide an assessment to the user.
 21. A computer readable medium having software modules for performing the method of claim 1 comprising the acts of: (a) comparing gene expression data obtained from a patient sample for a plurality of genes selected from Table 2, Table 3, and Table 4 or combinations thereof with a reference; and (b) providing a predictor score to a physician for use in determining an appropriate therapeutic regimen for a patient.
 22. A computer system, having a processor, memory, external data storage, input/output mechanisms, a display, for performing the method of claim 1, comprising: (a) a database; (b) logic mechanisms in the computer for generating the transcriptional profile index; and (c) a comparing mechanism in the computer for comparing the gene expression reference to expression data from a patient sample or an RNA sample from such a patient sample to calculate a predictor score.
 23. An internet accessible portal for providing biological information constructed and arranged to execute a computer-implemented method of claim 1 for providing: (a) a comparison of gene expression data of a plurality of genes of claim 1 in a patient sample with a transcriptional profile index; and (b) providing a predictor score to a physician for use in determining an appropriate therapeutic regime for a patient. 